title: CB-V-EL38-B

first: Run-Ze

address: No.20 Nanxincun, Xiangshan, Haidian District

department: Institute of Botany

institute: Chinese Academy of Sciences

data_processing:
Bowtie2 v2.2.5 was used to map clean reads to reference, allowing no more than two nucleotides mismatched.
Level of gene expression was calculated using the FPKM (expected fragments per kilobase of transcript per million fragments mapped) method.
Genome_build: Vitis vinifera  (PN40024) genome V2 download from Grape Genome Database (CRIBI)
Supplementary_files_format_and_content: excel file (.xlsx) include FPKM values for each sample

organism: Vitis vinifera

source_name: grape berries

growth_protocol: The own-rooted vines in this vineyard were planted in 2000, arranged in north–south rows with 2.5 m × 1 m vine spacing and equipped with a furrow irrigated system, spur-pruned (15 nodes per linear metre) and trained to a modified Vertical-Shoot-Positioned (M-VSP) trellis system. Nutrition and pest managements were carried out according to industry standards for this cultivar and the region as described previously.

extract_protocol:
A sub-sample of 50 berries were randomly selected from each biological replicate for RNA extraction. Total RNAs for RNA-seq analysis were isolated from frozen deseeded berries using a Plant Total RNA Extraction Kit (Sigma, St. Louis, MO, USA), and further purified by DNase I (Promega, Madison, WI, USA) digestion. RNA integrity and concentration were analyzed using the Nanodrop 2000 spectrophotometer (Thermo Fisher Scientific Inc., Wilmington, DE, USA) and the Aglient 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA).
cDNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For cluster bagging treatment, an individual cluster was placed into a two-layer kraft paper bags (36 × 36 cm), yellow exterior layer with the black interior layer coated with wax), with a bent straw to keep ventilation inside the bag. Each treatment was arranged in a completely randomized experimental design with three biological replicates. In each biological replicate, treatments were applied to 15 vines randomly selected from both south and north sites of the vineyard.

tag: cultivar

value: Cabernet Sauvignon

value: berries

tag: developmental stage

value: cluster bagging during verasion


title: CB-V-EL37-C

status: Public on Nov 25 2019

type: SRA

city: Beijing

last: Sun

country: China

library_source: transcriptomic

molecule: total RNA

tag: tissue

tag: treatment


title: CRMM1.miCLIP-seq.rep1

first: Bao-Fa

address: Da-Tun Road

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

data_processing:
For RNA-seq and MeRIP-seq, reads were processed using Cutadapt software (version 1.18) and Trimmomatic (version 0.36). The remained reads were aligned to human genome (version hg19) using Hisat2 (version 2.1.0).
For MeRIP-seq data, MACS2 software (version 2.0.10) was used for m6A peak calling, and m6A peaks were annotated by perfroming BEDTools’ intersectBed (version 2.27.1).
For miCLIP-seq, pre-processing was performed by using CLIP Tool Kit (CTK). The remined reads were aligned to human genome (version hg19) using BWA software (version 0.7.10).
m6A locus were detected by performing Program CIMS.pl for miCLIP-seq data.
miCLIP-seq m6A locus were annotated by using BEDTools’ intersectBed (version 2.27.1).
Genome_build: hg19
Supplementary_files_format_and_content: miCLIP-seq_m6A_single-nucleotide-resolution_locus.xlsx.gz: miCLIP-seq_m6A_single-nucleotide-resolution_locus
Supplementary_files_format_and_content: MeRIP-seq_m6A_peak_locus.xlsx.gz: MeRIP-seq_m6A_peak_locus
Supplementary_files_format_and_content: Reads_count_featureCounts.xlsx.gz: Reads count for all samples

molecule: polyA RNA

organism: Homo sapiens

source_name: Ocular melanoma cell line

extract_protocol:
For RNA-seq, total RNA was extracted from samples using an EZ-press RNA Purification Kit (B0004).
For miCLIP-seq, mRNA was isolated from tumor and normal cell lines by using Dynabeads mRNA Purification Kit (Life Technologies, 61006).
For RNA-seq, libraries were constructed from  100 ng of total RNA using an Illumina TruSeq RNA Sample Prep Kit (San Diego, CA, USA) following the manufacturer’s protocol.
For MeRIP-seq, purified mRNA was randomly fragmented to approximately 100 nucleotides using Ambion RNA fragmentation reagents and then subjected to IP with an anti-m6A antibody (202003, Synaptic Systems) and protein A magnetic beads (88845, Pierce) in meRIP buffer (150 mM NaCl, 10 mM Tris-HCl, pH 7.4, 0.1% NP-40) supplemented with RNase inhibitor. m6A-containing mRNA fragments were eluted with m6A in MeRIP buffer and purified using TRIzol reagent.
For miCLIP-seq, mRNA was fragmented to ~100 nucleotides using fragmentation reagent (Life Technologies, AM8740), and incubated with 5 µg of an anti-m6A antibody (Abcam, ab151230) in 450 µL of IP buffer (50 mM Tris, 100 mM NaCl, 0.05% NP-40, adjusted to pH 7.4) under gentle rotation at 4°C for 2 h. The mixture was transferred to a clear flat-bottom 96-well plate (Corning) on ice and irradiated three times with 0.15 J/cm2 at 254 nm using a CL-1000 Ultraviolet Crosslinker (UVP). After irradiation, the mixture was collected and incubated with 50 µL of prewashed Dynabeads Protein A (Life Technologies, 1001D) at 4°C for 2 h. After extensive washing twice with high-salt buffer (50 mM Tris, 1 M NaCl, 1 mM EDTA, 1% NP-40, 0.1% SDS, adjusted to pH 7.4) and twice with IP buffer, the samples on the beads were subjected to dephosphorylation with T4 PNK (NEB, M0201L) at 37°C for 20 min. The RNA was then eluted from the beads by proteinase K (Sigma, P2308) treatment at 55°C for 1 h, followed by phenol-chloroform extraction and ethanol precipitation. The purified RNA was subjected to library construction using SMARTer smRNA-Seq Kit for Illumina (Clontech Laboratories, 635030) according to the manufacturer’s instructions.

value: Ocular melanoma cell


title: ZYB_Normal

type: RNA

city: Guangzhou

first: hu

middle: xue

last: ting

address: NO.107 Yanjiangxi Road  Guangzhou

institute: Huxueting

description: Gene expression data

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays (6x7K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Axon GenePix 4000B Scanner.

data_processing: Quantile normalization and subsequent data processing were performed using the R software package. Differentially expressed circRNAs with statistical significance between two groups were identified through Volcano Plot filtering. Differentially expressed circRNAs between two samples were identified through Fold Change filtering. Hierarchical Clustering was performed to show the distinguishable circRNAs expression pattern among samples.

source_name: ZYB_adjacent non-cancerous tissues

label_protocol: total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing random primer according to Arraystar’s Super RNA Labeling protocol (Arraystar Inc.)

extract_protocol: Total RNA from each sample was quantified using the NanoDrop ND-1000. The sample preparation and microarray hybridization were performed based on the Arraystar’s standard protocols

treatment_protocol: Surgical resection of esophageal cancer tissue and corresponding adjacent tissues, immediately placed in liquid nitrogen preservation

value: Normal esophageal epithelial tissue


title: CB-V-EL37-A


title: CON_CD8_8

status: Public on Nov 26 2019

type: genomic

city: Pittsburgh

first: Amr

last: Sawalha

state: PA

address: 4401 Penn Avenue

country: USA

institute: University of Pittsburgh

description: healthy CD8+ T cell

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: Methylation beta values were calculated from raw intensity values using GenomeStudio Methylation module software (Illumina; ver 1.9.0) after subtracting background, normalization to control probes, error correction using the Illumina custom model, and correction for false discovery rate.

label: biotin

molecule: genomic DNA

source_name: CD8+ T cell DNA

label_protocol: standard Illumina protocol

extract_protocol: Peripheral blood mononuclear cells (PBMCs) were extracted from whole blood via Ficoll-Paque PLUS density centrifugation (GE Healthcare Bio-Sciences). Total T cells were isolated using negative selection by magnetic bead separation with the Human Pan T cell Isolation II kit (Miltenyi Biotec). Flow cytometry sorting was used to isolate CD3+CD56-TCRab+CD8+ T cells using the following fluorophore-conjugated antibodies: APC anti-human CD56 (clone: HCD56), FITC anti-human CD8a (clone: RPA-T8), Pacific Blue anti-human CD3 (clone: HIT3a), and PE anti-human alpha/beta-TCR (clone: IP26) (BioLegend). DNA was extracted from CD8+ T cells using the DNeasy Blood and Tissue kit (Qiagen) and bisulfite converted with the EZ DNA Methylation kit (Zymo Research) for DNA methylation analysis.

tag: cell type

value: CD8+ T cell

tag: disease status

value: healthy


title: CON_CD8_3

description: healthy CD8+ T cell


title: SLE_CD8_7

description: lupus CD8+ T cell

value: lupus


title: CB-V-EL38-C


title: CB-V-EL37-B


title: CB-V-EL36-B


title: CON_CD8_4

description: healthy CD8+ T cell


title: CON_CD8_6

description: healthy CD8+ T cell


title: CB-V-EL36-A


title: CB-FH-EL38-B

value: cluster bagging from fruit-set until harvest


title: CB-FH-EL38-C


title: CB-FH-EL38-A


title: CB-FH-EL37-C


title: CON_CD8_2

description: healthy CD8+ T cell


title: SLE_CD8_6

description: lupus CD8+ T cell


title: CB-FH-EL37-B


title: CB-FH-EL37-A


title: CB-V-EL38-A


title: CB-FH-EL36-B


title: CON_CD8_7

description: healthy CD8+ T cell


title: CB-FH-EL36-A


title: CB-FH-EL35-C


title: SLE_CD8_5

description: lupus CD8+ T cell


title: CB-FH-EL36-C


title: CB-FH-EL35-B


title: CB-FH-EL35-A


title: CB-FH-EL31-C


title: SLE_CD8_1

description: lupus CD8+ T cell


title: CB-FH-EL31-A


title: CB-FH-EL31-B


title: SLE_CD8_8

description: lupus CD8+ T cell


title: SLE_CD8_4

description: lupus CD8+ T cell


title: CON_CD8_1

description: healthy CD8+ T cell


title: CK-EL35-B

value: CK


title: CK-EL35-C


title: CK-EL31-C


title: CK-EL31-A


title: CK-EL35-A


title: CK-EL29-C


title: SLE_CD8_3

description: lupus CD8+ T cell


title: CK-EL29-B


title: CK-EL31-B


title: CK-EL29-A


title: SLE_CD8_2

description: lupus CD8+ T cell


title: CD4 Keap1 KO control 3

city: Baltimore

first: Sanjeev

last: Noel

address: Broadway

institute: Johns Hopkins

description:
KO9 (9/13/17)
CD4 Keap1 KO on C57BL6/J background
processed data file: genes.fpkm_table.txt

data_processing:
Paired-end 36nt sequencing on Illumina NextSeq 500.
Base calling with RTA version 2.4.11.
Data filtering to strip adapters with bcl2fastq 2.17.1.14.
Using Tophat version 2.1.0.and Cufflinks version 2.2.1 with default parameters (28), raw data were aligned to the GRCm38 mouse reference genome and Fragments Per Kilobase Of Exon Per Million (FPKM) values were obtained.
Included linear FPKM values were log2 converted (FPKM = 0 ignored) and quantile normalized with Partek Genomics Suite v7.0 WT versus WT-IRI compared by t-test.
Genome_build: GRCm38 mouse reference genome
Supplementary_files_format_and_content: genes.fpkm_table.txt: Tab-delimited text file includes FPKM values.

organism: Mus musculus

source_name: Kidney CD4 T cell

growth_protocol: WT C57BL6/J mice were purchased from Jackson laboratory. CD4 Keap1 KO mice were generated in house.

extract_protocol:
Kidney mononuclear cells were prepared using percoll gradient and CD4 T cells were flow sorted from IRI and control mice. Total RNA was isolated from flow sorted pure CD4 T cells using QIAGEN RNeasy and RNeasy micro kits.
Illumina NextSeq 500 compatible libraries were prepared using SMARTer® Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian kit (Takara, Mountain View, CA) with 1 ng of total RNA.
Libraries were multiplexed and sequenced with 60 million 36 base-pair paired-end reads per sample using two flowcell lanes.

treatment_protocol: Both WT C57BL6/J and CD4 Keap1 KO mice were subjected to 30 minute bilateral renal ischemia reperfusion surgery. Separate group of mice from both genotype were used as respective control. Both right and left renal padicles were clamped for 30 minutes to induce ischemia after which clamps were removed and kidneys allowed to reperfuse. Kidneys were harvested 24 hours after ischemia reperfusion injury and CD4 T cells flow sorted for RNA seq analysis.

tag: strain/background

tag: genotype/variation

value: CD4 Keap1 KO

value: Kidney CD4 T cells

tag: experimental group

value: Control


title: CD4 Keap1 KO IRI 3

description:
KO12 (9/13/17)
CD4 Keap1 KO on C57BL6/J background
processed data file: genes.fpkm_table.txt

value: IRI


title: CD4 Keap1 KO control 2

description:
KO8 (9/13/17)
CD4 Keap1 KO on C57BL6/J background
processed data file: genes.fpkm_table.txt


title: WT IRI 2

description:
WT5 (9/13/17)
WT C57BL6/J
processed data file: genes.fpkm_table.txt

value: WT


title: CD4 Keap1 KO control 1

description:
KO7 (9/13/17)
CD4 Keap1 KO on C57BL6/J background
processed data file: genes.fpkm_table.txt


title: WT control 3

description:
WT3 (9/13/17)
WT C57BL6/J
processed data file: genes.fpkm_table.txt


title: G2_chronic stressed contralateral

city: Berlin

first: Stephanie

last: Wegner

address: Charitéplatz 1

department: Experimental Neurology

country: Germany

institute: Charité - Universitätsmedizin Berlin

description: chronic_stressed_ipsi_vs._chronic_stressed_contra.xlsx

data_processing:
Demultiplexing of all libraries for each sequencing lane using Illumina bcl2fastq 2.17.1.14
Clipping of sequencing adapter remnants from all raw reads
Combination of forward and reverse reads using BBMerge 34.48
SMRT concatamer adapter detection and read splitting
Filtering of rRNA sequencing using RiboPicker 0.4.3, Filtering of poly-A reads
Alignment against reference with STAR 2.4.1b
Counting of STAR-aligned reads with htseq-count
Differential expression analysis with cuffdiff 2.1.1
Genome_build: GRCm38 ENSEMBL release 84
Supplementary_files_format_and_content: Excel files include read count for each gene per sample

source_name: brain endothelial cells

extract_protocol:
After sacrificing brains were removed, stroke lesion area and the corresponding contralateral area were isolated. CD31+ cells from these tissues were first enriched with the MACS technique. Afterwards followed an isolation of CD45-/DAPI-/CD31+/CD146+ single cells by flow cytometry. RNA isolation was performed with the NucleoSpin® XS Kit (MACHEREY-NAGEL; Prod#: 740902.50).
The library construction was performed with the Encore Rapid DR Multiplex system from NuGen Technologies, Inc. according to the manual.

tag: strain

tag: cells

value: brain endothelial cells

tag: age

value: 14 weeks

tag: genotyp

value: wild type

tag: condition

value: chronic stressed


title: H1_control ipsilateral

value: control


title: CD4 Keap1 KO IRI 2

description:
KO11 (9/13/17)
CD4 Keap1 KO on C57BL6/J background
processed data file: genes.fpkm_table.txt


title: G1_chronic stressed ipsilateral


title: CD4 Keap1 KO IRI 1

description:
KO10 (9/13/17)
CD4 Keap1 KO on C57BL6/J background
processed data file: genes.fpkm_table.txt


title: F2_chronic stressed contralateral


title: H2_control contralateral


title: WT control 1

description:
WT1 (9/13/17)
WT C57BL6/J
processed data file: genes.fpkm_table.txt


title: F1_chronic stressed ipsilateral


title: E2_control contralateral


title: E1_control ipsilateral


title: D2_control contralateral


title: C2_chronic stressed contralateral


title: WT IRI 3

description:
WT6 (9/13/17)
WT C57BL6/J
processed data file: genes.fpkm_table.txt


title: WT control 2

description:
WT2 (9/13/17)
WT C57BL6/J
processed data file: genes.fpkm_table.txt


title: C1_chronic stressed ipsilateral


title: B1_chronic stressed ipsilateral


title: WT IRI 1

description:
WT4 (9/13/17)
WT C57BL6/J
processed data file: genes.fpkm_table.txt


title: B2_chronic stressed contralateral


title: A2_control contralateral


title: A1_control ipsilateral


title: HT1080_Repliseq_early_rep1

city: Worcester

first: George

last: Spracklin

state: Massachusetts

address: 368 Plantation Street

department: Systems Biology

institute: University of Massachusetts Medical School

description:
processed data file:
2stateHMM_Repliseq_HT1080_mergedreplicates_E_L.25000.log2ratio.bw_2state_HMM.bed
Repliseq_HT1080_mergedreplicates_E_L.25000.log2ratio.bw

library_source: genomic

data_processing:
FASTQ files were trimmed and assessed for quality with fastp.
Trimmed reads were mapped to hg38 (UCSC) using bwa mem.
Alignment files (BAM format) were filtered using encode_filter.py
Replicate filtered BAM files were merged using sambamba.
Signal tracks were generated using 100bp bins and normalized to reads per genomic coverage (RPGC) using deeptools bamcoverage with the following parameters: -bs 100 -of bigwig --effectiveGenomeSize 2913022398 --normalizeUsing RPGC -e.
Differential signal tracks (log2ratio) were generated using deeptools bamcompare. Published data (fastq files) were downloaded from GEO and processed as described above.
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig files were generated using deeptools. Scores represent as either log2ratio(signal/input) or reads per genomic content (RPGC). Domains (BED file) were called with HMMs.

growth_protocol: HCT116 and DKO cells were cultured in McCoy5A media. DKO cells were grown in the presence of G418, geneticin. HT1080 cells were cultured in DMEM media with L-glutamine. All media was supplemented with 10% FBS  at 37C/5%CO2

extract_protocol:
Cells were grown to ~75% confluency, harvested with trypsin, washed in 1X PBS, and frozen/stored at -80°C. Thawed cells were fixed in 1% formaldehyde and quenched in 0.125M Glycine, then washed twice in 1X PBS. Fixed cells were then resuspended in 500ul lysis buffer (50mM Tris-HCl pH 8.0, 10mM NaCl, 0.2% NP40, 1X PITC) for 30 min on ice with periodic resuspension.
Libraries were prepared using NEB UltraII DNA library kit

tag: cell line

value: fibrosarcoma

tag: cell line source gender

value: male

tag: library strategy

value: Repli-seq

tag: chip antibody

value: anti-BrdU (BD:555627)


title: DKO_ChIPseq_H3_rep1

description:
processed data file:
ChIPseq_DKO_rep1_H3.sort.hg38.nodup.bam.coverage_RPGCe.bw.25kb.log2ratio.bw.2state_1_state.bed
ChIPseq_DKO_rep1_H3.sort.hg38.nodup.bam.coverage_RPGCe.bw.25kb.log2ratio.bw

value: DKO

value: colon cancer cell line

value: ChIP-seq


title: DKO_ChIPseq_HP1beta_rep1

description:
processed data file:
ChIPseq_DKO_rep1_HP1beta.sort.hg38.nodup.bam.coverage_RPGCe.bw.25kb.log2ratio.bw.2state_1_state.bed
ChIPseq_DKO_rep1_HP1beta.sort.hg38.nodup.bam.coverage_RPGCe.bw.25kb.log2ratio.bw

value: anti-HP1beta (CST:8676S)


title: HT1080_Repliseq_late_rep2


title: HT1080_Repliseq_late_rep1


title: CB-V-EL36-C

tag: cultivar

value: Cabernet Sauvignon

value: berries

tag: developmental stage

value: cluster bagging during verasion


title: D1_control ipsilateral


title: DKO_ChIPseq_Input_rep1


title: HCT116_ChIPseq_H3K9me3_rep1

description:
processed data file:
ChIPseq_HCT116_rep1_K9me3.sort.hg38.nodup.bam.coverage_RPGCe.bw.25kb.log2ratio.bw.2state_1_state.bed
ChIPseq_HCT116_rep1_K9me3.sort.hg38.nodup.bam.coverage_RPGCe.bw.25kb.log2ratio.bw


title: HCT116_ChIPseq_H3_rep1

description:
processed data file:
ChIPseq_HCT116_rep1_H3.sort.hg38.nodup.bam.coverage_RPGCe.bw.25kb.log2ratio.bw.2state_1_state.bed
ChIPseq_HCT116_rep1_H3.sort.hg38.nodup.bam.coverage_RPGCe.bw.25kb.log2ratio.bw


title: HCT116_ChIPseq_HP1beta_rep1

description:
processed data file:
ChIPseq_HCT116_rep1_HP1beta.sort.hg38.nodup.bam.coverage_RPGCe.bw.25kb.log2ratio.bw.2state_1_state.bed
ChIPseq_HCT116_rep1_HP1beta.sort.hg38.nodup.bam.coverage_RPGCe.bw.25kb.log2ratio.bw


title: DKO_ChIPseq_H3K9me2_rep1

description:
processed data file:
ChIPseq_DKO_rep1_K9me2.sort.hg38.nodup.bam.coverage_RPGCe.bw.25kb.log2ratio.bw.2state_1_state.bed
ChIPseq_DKO_rep1_K9me2.sort.hg38.nodup.bam.coverage_RPGCe.bw.25kb.log2ratio.bw


title: DKO_ChIPseq_HP1alpha_rep1

description:
processed data file:
ChIPseq_DKO_rep1_HP1alpha.sort.hg38.nodup.bam.coverage_RPGCe.bw.25kb.log2ratio.bw.2state_0_state.bed
ChIPseq_DKO_rep1_HP1alpha.sort.hg38.nodup.bam.coverage_RPGCe.bw.25kb.log2ratio.bw

value: anti-HP1alpha (CST:2616)


title: HCT116_ChIPseq_H3K9me2_rep1

description:
processed data file:
ChIPseq_HCT116_rep1_K9me2.sort.hg38.nodup.bam.coverage_RPGCe.bw.25kb.log2ratio.bw.2state_1_state.bed
ChIPseq_HCT116_rep1_K9me2.sort.hg38.nodup.bam.coverage_RPGCe.bw.25kb.log2ratio.bw


title: HCT116_ChIPseq_Input_rep1


title: HCT116_ChIPseq_HP1alpha_rep1

description:
processed data file:
ChIPseq_HCT116_rep1_HP1alpha.sort.hg38.nodup.bam.coverage_RPGCe.bw.25kb.log2ratio.bw.2state_1_state.bed
ChIPseq_HCT116_rep1_HP1alpha.sort.hg38.nodup.bam.coverage_RPGCe.bw.25kb.log2ratio.bw


title: DKO_ChIPseq_H3K9me3_rep1

description:
processed data file:
ChIPseq_DKO_rep1_K9me3.sort.hg38.nodup.bam.coverage_RPGCe.bw.25kb.log2ratio.bw.2state_1_state.bed
ChIPseq_DKO_rep1_K9me3.sort.hg38.nodup.bam.coverage_RPGCe.bw.25kb.log2ratio.bw


title: HT1080_ChIPseq_H3K27me3_rep2

description:
processed data file:
ChIPseq_HT1080_H3K27me3_mergedreplicates.sort.hg38.nodup.bam.coverage_RPGCe_.bw.log2ratio.bw_2state_1_state.bed
ChIPseq_HT1080_H3K27me3_mergedreplicates.sort.hg38.nodup.bam.coverage_RPGCe_.bw.log2ratio.bw


title: HT1080_ChIPseq_H3K9me2_rep2

description:
processed data file:
ChIPseq_HT1080_H3K9me2_mergedreplicates.sort.hg38.nodup.bam.coverage_RPGCe_.bw.log2ratio.bw_2state_0_state.bed
ChIPseq_HT1080_H3K9me2_mergedreplicates.sort.hg38.nodup.bam.coverage_RPGCe_.bw.log2ratio.bw


title: HT1080_ChIPseq_HP1alpha_rep2

description:
processed data file:
ChIPseq_HT1080_HP1_mergedreplicates.sort.hg38.nodup.bam.coverage_RPGCe_.bw.log2ratio.bw_2state_1_state.bed
ChIPseq_HT1080_HP1_mergedreplicates.sort.hg38.nodup.bam.coverage_RPGCe_.bw.log2ratio.bw


title: HT1080_ChIPseq_CTCF_rep2

description:
processed data file:
ChIPseq_HT1080_CTCF_mergedreplicates.sort.hg38.nodup.bam.coverage_RPGCe.bw

value: anti-CTCF (CST:#3418)


title: HT1080_ChIPseq_HP1alpha_rep1


title: HT1080_ChIPseq_Input_rep2

description: processed data file:


title: HT1080_Repliseq_early_rep2


title: HT1080_ChIPseq_H3K9me3_rep1

description:
processed data file:
ChIPseq_HT1080_H3K9me3_mergedreplicates.sort.hg38.nodup.bam.coverage_RPGCe_.bw.log2ratio.bw_2state_1_state.bed
ChIPseq_HT1080_H3K9me3_mergedreplicates.sort.hg38.nodup.bam.coverage_RPGCe_.bw.log2ratio.bw


title: HT1080_ChIPseq_CTCF_rep1


title: HT1080_ChIPseq_H3K9me2_rep1


title: HT1080_ChIPseq_Input_rep1


title: HT1080_Protectseq_rep2

description:
processed data file:
3stateHMM_Protectseq_HT1080_merge_mapq0.merged.sort.hg38.nodup.bam.coverage_RPGCe_25000.bw.log2ratio.bw_3state_combined_state.bed
2stateHMM_Protectseq_HT1080_merge_mapq0.merged.sort.hg38.nodup.bam.coverage_RPGCe_25000.bw.log2ratio.bw_1_state.bed
Protectseq_HT1080_merge_mapq0.merged.sort.hg38.nodup.bam.coverage_RPGCe_25000.bw.log2ratio.bw

value: Protect-seq


title: HT1080_Protectseq_rep3


title: HT1080_WGS_input

value: WGS


title: HT1080_Protectseq_rep1


title: DKO_WGS_input


title: DKO_Protectseq_rep2

description:
processed data file:
3stateHMM_Protectseq_DKO_merge.mapq0.merged.sort.hg38.nodup.bam.coverage_RPGCe_25000.bw.log2ratio.bw.3state_combined_state.bed
2stateHMM_Protectseq_DKO_lad_merge_mapq0.merged.sort.hg38.nodup.bam.coverage_RPGCe_25000.bw.log2ratio.bw_2state_0_state.bed
Protectseq_DKO_merge_mapq0.merged.sort.hg38.nodup.bam.coverage_RPGCe_25000.bw.log2ratio.bw


title: DKO_Protectseq_rep1


title: ZCCHC4_knockout_haploid_rep2

city: Bern

first: Yeji

last: Kim

address: Freiestrasse 3

department: Department of Chemistry and Biochemistry

country: Switzerland

institute: University of Bern

data_processing:
Adaptors were clipped and trimmed using FASTx toolkit
Reads were aligned to human rRNA to remove rRNA-derived reads and mapped to the human genome hg38 using bowtie
Reads for each individual transcript were counted using a custom script
Genome_build: hg38
Supplementary_files_format_and_content: CSV file containing raw counts per transcript for the five different samples

source_name: haploid cells

extract_protocol:
Cells were washed with ice-cold PBS and flash frozen in liquid nitrogen. Subsequently, the dish was transferred to ice, 400 µl lysis buffer (10 mM Tris-HCl pH 7.5, 100 mM NaCl, 5 mM MgCl2, 1 % Triton X-100, 0.5 mM DTT, 0.5 % deoxycholate (w/v) and 100 µg/ml CHX) was dripped onto the cells and cells were scraped after lysis buffer had thawed. Next, samples were centrifuged for 5 min at 4 °C and 10,000 g.
Ribosome protected fragments were generated by digesting 10 A260 units of the cleared lysate with 900 U RNase I (ThermoFisher) at 22 °C. The reaction was stopped after 1 h by addition of 15 µl SuperaseIn (ThermoFisher) and loaded on a 10-50% (w/v) sucrose gradient in 50 mM Tris pH 7.5, 50 mM NH4Cl, 12 mM MgCl2, 0.5 mM DTT, 100 µg/ml CHX and centrifuged for 3 h at 35,000 rpm and 4 °C in a TH-641 rotor (Thermo Scientific). Monosomes were fractionated and total RNA isolated. Subsequently,RNA was separated on 15% polyacrylamide gels (8 M urea, 1 x TBE) and 28-32nt ribosome footprints were extracted from the gel. Finally, libraries were generated as described by Ingolia and coworkers (Ingolia et al. 2012) but using adenylated 3’-adapters that contained 4 randomized nucleotides to reduce ligation biases (Lecanda et al. 2016).

value: HAP1 cells

tag: genotype

value: ZCCHC4 knockout


title: ZCCHC4_knockout_haploid_rep3


title: HCT116_Protectseq_rep1

description:
processed data file:
3state_Protectseq_HCT116_merge_mapq0.merged.sort.hg38.nodup.bam.coverage_RPGCe_25000.bw.log2ratio.bw_combined_state.bed
2stateHMM_Protectseq_HCT116_lad_merge_mapq0.merged.sort.hg38.nodup.bam.coverage_RPGCe_25000.bw.log2ratio.bw_2state_0_state.bed
Protectseq_HCT116_merge_mapq0.merged.sort.hg38.nodup.bam.coverage_RPGCe_25000.bw.log2ratio.bw

tag: cell type


title: HT1080_ChIPseq_H3K9me3_rep2

value: fibrosarcoma


title: Luteolin_replicate2

city: Kyoto

first: Seiji

last: Masuda

state: Kyoto

address: Kitashirakawa Oiwakecho, Sakyo-ku

country: Japan

institute: Division of Integrated Life Sciences, Graduate School of Biostudies

description:
Luteolin_6_S6
processed data file:
DMSO_vs_Luteolin_A3SS.MATS.ReadsOnTargetAndJunctionCounts
DMSO_vs_Luteolin_A5SS.MATS.ReadsOnTargetAndJunctionCounts
DMSO_vs_Luteolin_MXE.MATS.ReadsOnTargetAndJunctionCounts
DMSO_vs_Luteolin_RI.MATS.ReadsOnTargetAndJunctionCounts
DMSO_vs_Luteolin_SE.MATS.ReadsOnTargetAndJunctionCounts

data_processing:
Reads were aligned to hg38 genome using STAR (version-2.5.2b)
Alternative splicing analysis was performed using rMATS (version-3.2.5)
Genome_build: hg38
Supplementary_files_format_and_content: txt files were generate using rMATS (version-3.2.5)

growth_protocol: U2OS cells were grown in Dulbecco's modified Eagle medium containing 10% fatal bovine serum

extract_protocol:
U2OS cells (20% confluency) treated with DMSO or apigenin or luteolin were recovered by trypsinization. Total RNA was isolated by Sepasol-RNA I super G (Nacalai tesque, Japan) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Apigenin or luteolin was treated at a concentration of 75μM

tag: treatment

value: Luteolin


title: HCT116_Protectseq_rep3

value: male


title: Luteolin_replicate1

description:
Luteolin_5_S5
processed data file:
DMSO_vs_Luteolin_A3SS.MATS.ReadsOnTargetAndJunctionCounts
DMSO_vs_Luteolin_A5SS.MATS.ReadsOnTargetAndJunctionCounts
DMSO_vs_Luteolin_MXE.MATS.ReadsOnTargetAndJunctionCounts
DMSO_vs_Luteolin_RI.MATS.ReadsOnTargetAndJunctionCounts
DMSO_vs_Luteolin_SE.MATS.ReadsOnTargetAndJunctionCounts


title: ZCCHC4_knockout_haploid_rep1


title: HT1080_ChIPseq_H3K27me3_rep1


title: Wildtype_haploid_rep2

value: Wild type


title: Wildtype_haploid_rep1


title: DMSO_replicate2

description:
DMSO_2_S2
processed data file:
DMSO_vs_Apigenin_A3SS.MATS.ReadsOnTargetAndJunctionCounts
DMSO_vs_Apigenin_A5SS.MATS.ReadsOnTargetAndJunctionCounts
DMSO_vs_Apigenin_MXE.MATS.ReadsOnTargetAndJunctionCounts
DMSO_vs_Apigenin_RI.MATS.ReadsOnTargetAndJunctionCounts
DMSO_vs_Apigenin_SE.MATS.ReadsOnTargetAndJunctionCounts
DMSO_vs_Luteolin_A3SS.MATS.ReadsOnTargetAndJunctionCounts
DMSO_vs_Luteolin_A5SS.MATS.ReadsOnTargetAndJunctionCounts
DMSO_vs_Luteolin_MXE.MATS.ReadsOnTargetAndJunctionCounts
DMSO_vs_Luteolin_RI.MATS.ReadsOnTargetAndJunctionCounts
DMSO_vs_Luteolin_SE.MATS.ReadsOnTargetAndJunctionCounts

tag: cell lie

value: DMSO


title: Apigenin_replicate2

description:
Apigenin_4_S4
processed data file:
DMSO_vs_Apigenin_A3SS.MATS.ReadsOnTargetAndJunctionCounts
DMSO_vs_Apigenin_A5SS.MATS.ReadsOnTargetAndJunctionCounts
DMSO_vs_Apigenin_MXE.MATS.ReadsOnTargetAndJunctionCounts
DMSO_vs_Apigenin_RI.MATS.ReadsOnTargetAndJunctionCounts
DMSO_vs_Apigenin_SE.MATS.ReadsOnTargetAndJunctionCounts

value: Apigenin


title: HCT116_Protectseq_rep2

value: colon cancer cell line


title: H3K27ac ChIP-seq 1

city: Cleveland

first: Peter

last: Scacheri

state: OH

address: 2109 Adelbert Road

department: Genetics and Genome Sciences

institute: Case Western Reserve University

data_processing:
Reads were quality and adapter trimmed using Trim Galore! Version  0.4.1.
Trimmed reads were alighed to hg19 with Bowtie2 version 2.3.2.
Duplicate reads (potential artifacts of PCR in library preparation) were removed using Picard MarkDuplicates.
Peaks were called with MACS version 2.1.1 to define broad peaks.
Genome_build: hg19
Supplementary_files_format_and_content: bigWIG files were generated using bamCoverage with reads per genome coverage normalization. BED files in a broadPeaks format from MACS2.

source_name: primary Wilms tumor sample

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according previous methods (e.g. Schmidt et al. Methods 2009). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina MiSeq 500 following the manufacturer's protocols using 75 bp single end reads.

tag: tissue

value: primary Wilms tumor sample

value: rabbit anti-H3K27ac (Abcam #4729)


title: Apigenin_replicate1

description:
Apigenin_3_S3
processed data file:
DMSO_vs_Apigenin_A3SS.MATS.ReadsOnTargetAndJunctionCounts
DMSO_vs_Apigenin_A5SS.MATS.ReadsOnTargetAndJunctionCounts
DMSO_vs_Apigenin_MXE.MATS.ReadsOnTargetAndJunctionCounts
DMSO_vs_Apigenin_RI.MATS.ReadsOnTargetAndJunctionCounts
DMSO_vs_Apigenin_SE.MATS.ReadsOnTargetAndJunctionCounts


title: DMSO_replicate1

description:
DMSO_1_S1
processed data file:
DMSO_vs_Apigenin_A3SS.MATS.ReadsOnTargetAndJunctionCounts
DMSO_vs_Apigenin_A5SS.MATS.ReadsOnTargetAndJunctionCounts
DMSO_vs_Apigenin_MXE.MATS.ReadsOnTargetAndJunctionCounts
DMSO_vs_Apigenin_RI.MATS.ReadsOnTargetAndJunctionCounts
DMSO_vs_Apigenin_SE.MATS.ReadsOnTargetAndJunctionCounts
DMSO_vs_Luteolin_A3SS.MATS.ReadsOnTargetAndJunctionCounts
DMSO_vs_Luteolin_A5SS.MATS.ReadsOnTargetAndJunctionCounts
DMSO_vs_Luteolin_MXE.MATS.ReadsOnTargetAndJunctionCounts
DMSO_vs_Luteolin_RI.MATS.ReadsOnTargetAndJunctionCounts
DMSO_vs_Luteolin_SE.MATS.ReadsOnTargetAndJunctionCounts


title: H3K27ac ChIP-seq 4


title: H3K27ac ChIP-seq 3


title: H3K27ac ChIP-seq 5


title: H3K27ac ChIP-seq 2


title: SATU1_99_S6_R1_001

city: Tartu

first: Hindrek

last: Teder

address: Tiigi 61b

country: Estonia

institute: The Competence Centre on Health Technologies

data_processing:
BCLs were converted to FASTQs using bcl2fastq2 (version 2.20) with 0 mismatches
Reads were converted to FASTA format, trimmed to 62 bp, shorter than 62 bp reads were removed using FASTX-Toolkit (version 0.0.14)
UMI subsequences were joined using AWK
Reads were demultiplexed by target sequence using FASTX-Toolkit with 5 mismatches
Target sequences were trimmed, reads with N nucleotide were removed using FASTX-Toolkit
Sequences were merged by UMI using FASTX-Toolkit
Read and molecule counts were calculated per sample and target using UMI thresholds 2
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file containing targeted read and molecule counts by locus and sample at fixed UMI thresholds

source_name: placenta

extract_protocol:
Placenta samples, stored snap fozen or in RNAlater (Thermo Fisher Scientific) in -80°C, were thawed and homogenized using the FastPrep®-24 5G Classic Instrument (2 x 30 s at 4.5 m/s) and Lysing Matrix D tubes  according to manufacturer's instructions (MP Biomedicals, Santa Ana, CA). Samples were lysed using 600 µl RTL buffer and 6 µl ß-mercaptoethanol on 20 mg of tissue homogenate, followed by RNA extraction using the RNeasy Mini Kit according to manufacturer's instructions (Qiagen, Valencia, CA). RNA concentrations were measured by the NanoDrop® 2000 UV-Vis Spectrophotometer (Thermo Fisher Scientific) and diluted in 10 ng/µl. The 2100 Bioanalyzer System (Agilent Technologies, Santa Clara, CA)  was utilized for measurement of RNA integrity (RIN) values. For most samples, the RIN values ranged from 7 to 8.8, but samples with the lower range of 4 to 6.9 gave highly comparable results in TAC assay testing, and were included in the final assays. RNA samples were quantitated with the Qubit® 2.0 Fluorometer using Invitrogen RNA HS Assay Kit (5 to 100 ng) or Invitrogen RNA BR Assay Kit (20 to 1000 ng) according to manufacturer's instructions  (Thermo Fisher Scientific).
Non-skirted low profile PCR Strip Tube Plate (Thermo Fisher) was used with domed cap strips (Thermo Fisher). 1 µl of total-RNA sample was used. The RIN values 7.7 – 9.6 were quantified by Qubit (Invitrogen) and diluted to concentration 90 ng/µl. RT master mix contained 1 µl of 1:50,000 of ERCC RNA Spike-In Mix 1 (Life Technologies) dilution for technical normalization. Altogether 169 TAC-seq detector pairs targeting biomarkers and ERCC spike-in molecules were previously mixed together from 100 µM stock solutions, creating a “100 µM” oligo pool. The mixture was diluted to 5 µM by water and stored at -20°C. 1 µl of total-RNA template for each individual library was added to 2 µl denaturation buffer, containing 5 mM Tris-HCl (pH 7.0) (Sigma-Aldrich), 1 mM dNTP mixture (Thermo Fisher), 400 nM Oligo-T30 primer and 0.05% Triton X-100 (Sigma-Aldrich). Reaction was mixed by pipetting and centrifuged briefly. RNA was denatured by 1 min at 80°C and placed on ice. After that, reverse transcriptase (RT) master mix containing 100 mM Tris-HCl (pH 8.5) (Sigma-Aldrich), 2.5 M betaine (Sigma-Aldrich), 150 mM KCl (Sigma-Aldrich), 10 mM DTT (Sigma-Aldrich), 15 mM MgCl (Sigma-Aldrich), 4 U RiboLock RNase inhibitor (Thermo Fisher) and 20 U Maxima H Minus Reverse Transcriptase (Thermo Fisher) was prepared. The content was mixed on vortex and centrifuged briefly. 2 µl of RT master mix was added to previously denatured RNA (3 µl). All RT pipetting steps were performed on ice. cDNA synthesis was performed by 30 min at 42°C, following 5 min at 85°C for RT inactivation.   Once cDNA synthesis was completed, 1 µl of 5 µM TAC-seq detector mixture was added to RT mixture. The content was mixed on vortex and centrifuged briefly. Strip tubes were placed on thermocycler, denatured 1 min at 98°C and following 1 h at 60°C to enable specific cDNA and TAC-seq probe hybridization. After hybridization, thermostable ligase reaction mixture was added on thermocycler, keeping a constant (60°C) hybridization temperature. The cycler lid was opened and strip caps were removed. 5 µl of Taq DNA ligase master mix, containing 2× Taq DNA ligation buffer (New England Biolabs, NEB) and 1 U Taq DNA ligase (NEB, cat no M0208) were added to each individual reaction tube and mixed by pipetting. The strip tubes were not removed from 60°C thermocycler to avoid self- and mispairing of TAC-seq probes. Ligation reaction was stopped after 20 min incubation by placing reaction plate on ice.   15 µl of previously combined Dynabeads MyOne Carboxylic Acid beads (2 µl) (Thermo Fisher) and 13 µl of capture buffer (30% PEG-6000 (Sigma-Aldrich), 2 M NaCl (Sigma-Aldrich), 5 mM Tris-HCl (pH 7.5) (Sigma-Aldrich), 10 mM EDTA (Sigma-Aldrich) and 0.02% Tween-20 (Sigma-Aldrich)) was added to ice-cooled ligated sample. The content was mixed by vortex. The capture was carried out for 10 min at RT, and after that the samples were placed on DynaMag-96 Side Magnet (Thermo Fisher) holding 8-well strip tubes on VersiPlate Frame (Thermo Fisher). The clean supernatant was removed. The beads on magnet were washed once with 50 µl fresh 80% ethanol. Ethanol was removed by pipetting, and the clean pellet, without ethanol drops, was dried for 2 min. Once beads were dry, strip tubes were removed from the magnet and 18 µl of PCR master mix was added directly to beads. The master mix contained 1× proofreading HOT FIREPol Blend Master Mix (SolisBiodyne, Tartu, Estonia) and 250 nM TAC-seq Left primer. In addition to universal TAC-seq Left, different TAC-seq barcode oligonucleotides were used to introduce a six-nucleotide barcode to each studied sample. For that, 2 µl of 5 µM TAC-seq Barcoded primers were added individually to each PCR reaction. Strip tubes were closed with clean domed caps, mixed on vortex until all beads were suspended. The ERCC spike-in reaction was incubated at 95°C for 12 min, followed by two cycles of 95°C for 20 s, 57°C for 60 s and 72°C for 20 s. In addition, 10 cycles of 95°C for 20 s, 65°C for 20 s and 72°C for 20 s with a final extension at 72°C for 1 min using the default ramp speed of the T100 cycler (Bio-Rad) were performed. PCR products were pooled together into 1.5 ml tube. The pooled tube was placed on magnet to remove carboxylated beads before the following column purification. Clear supernatant was purified with DNA Clean & Concentrator-5 column (Zymo Research) and eluted with 50 µl EB. The library was size-selected using AMPure XP beads (Beckman Coulter) in a single-step selection to reduce 81 bp linear PCR double-stranded by-product. 50 µl beads were added to 50 µl of the purified PCR product, incubated for 5 min at room temperature and captured by a magnet for 3 min. After incubation on magnet, the supernatant was discarded and the remaining beads were centrifuged at 500×g for 10 s. After centrifugation, the beads were placed again on the magnet and all remaining supernatant was removed. The beads were eluted directly without ethanol washing in 25 µl of EB and incubated for 1 min at RT. Finally, the eluted library was transferred to a clean tube after 1 min incubation on the magnet. The library (single 180 bp product) was visualized on a TapeStation High Sensitivity D1000 ScreenTape (Agilent Technologies) and quantified using KAPA Library Quantification Kit (Roche).  S1 TGAACT  S2 GATCTG  S3 ACATCG  S4 GCCTAA  S5 CGTGAT  S6 TGGTCA  S7 ACATGT  S8 ATTGGC  S9 CTGATC  S13 GTAGCC  S49 ATTCAG  S12 TCAAGT  S50 TACAAC  S14 TACAAG  S15 ATCAGT  S16 GCTCAT  S17 AGGAAT  S51 AACGAC  S52 GATTCC  S20 TGAGTG  S21 CGCCTG  S53 AAGCGA  S23 TGTTGG  S24 AGCATC  S25 GGTTGT  S26 CATTGT  S27 ACTCGT  S28 TATCGT  S29 CTTAGT  S30 TACTTG  S31 ATCGTG  S32 TCTCTG  S33 GTACTG  S34 ATGATG  S35 TCCATG  S36 TCGTTC  S37 GTTGTC  S38 AATGTC  S39 TATAGC  S40 CATTAC  S41 CAGGTA  S42 AGACTA  S43 CTCATA  S44 TGTAGA  S45 CTGTCA  S46 CTATCG  S47 GTAACG  S48 CGATAG
Illumina NextSeq 500 high output 75 cycles kit (Illumina, San Diego, CA) using 62 bp read-1 and 6 bp index reads.

tag: pre-eclampsia

value: severe

tag: gestational age (weeks)

tag: Sex

tag: ethnicity

value: Finnish


title: DKO_Protectseq_rep3

value: DKO


title: SATU3_98_S17_R1_001


title: SATU3_97_S18_R1_001


title: SATU2_96_S36_R1_001


title: SATU1_95_S3_R1_001

value: female


title: SATU4_94_S37_R1_001


title: SATU1_93_S14_R1_001


title: SATU5_87_S16_R1_001


title: SATU2_88_S16_R1_001


title: SATU1_85_S4_R1_001

value: no


title: SATU1_84_S23_R1_001

value: mild


title: SATU2_79_S10_R1_001


title: SATU1_78_S39_R1_001


title: SATU5_81-5_S2_R1_001


title: SATU1_74_S16_R1_001


title: SATU5_76-4_S3_R1_001


title: SATU2_90_S38_R1_001


title: SATU2_72_S20_R1_001


title: SATU2_71_S11_R1_001


title: SATU4_64_S19_R1_001


title: SATU1_68_S7_R1_001


title: SATU1_70_S10_R1_001


title: SATU2_65_S21_R1_001


title: SATU3_63_S2_R1_001


title: SATU5_67-5_S4_R1_001


title: SATU3_92_S19_R1_001


title: SATU3_62_S3_R1_001


title: SATU5_618-5_S37_R1_001


title: SATU5_617-5_S38_R1_001


title: SATU1_61_S29_R1_001


title: SATU5_616-5_S39_R1_001


title: SATU2_73_S12_R1_001


title: SATU2_77_S19_R1_001


title: SATU1_59_S11_R1_001


title: SATU2_58_S32_R1_001


title: SATU3_592_S38_R1_001


title: SATU3_563_S36_R1_001


title: SATU2_522_S24_R1_001


title: SATU2_56_S22_R1_001


title: SATU1_54_S35_R1_001


title: SATU1_521_S25_R1_001


title: SATU2_519_S2_R1_001


title: SATU4_517_S21_R1_001


title: SATU3_511_S20_R1_001


title: SATU3_515_S13_R1_001


title: SATU1_503_S37_R1_001


title: SATU5_613-5_S40_R1_001


title: SATU1_504_S48_R1_001


title: SATU3_50_S23_R1_001


title: SATU1_49_S19_R1_001


title: SATU1_46_S40_R1_001


title: SATU2_45_S25_R1_001


title: SATU2_39_S1_R1_001


title: SATU4_48_S20_R1_001


title: SATU2_580_S37_R1_001


title: SATU1_37_S12_R1_001


title: SATU5_60-5_S35_R1_001


title: SATU1_57_S18_R1_001


title: SATU4_31_S11_R1_001


title: SATU2_91_S40_R1_001


title: SATU5_32_S7_R1_001


title: SATU4_30_S34_R1_001


title: SATU1_26_S24_R1_001


title: SATU1_518_S36_R1_001


title: SATU4_24_S12_R1_001


title: SATU2_203_S3_R1_001


title: SATU2_202_S26_R1_001


title: SATU5_2017_S36_R1_001


title: SATU4_200_S26_R1_001


title: SATU1_51_S27_R1_001


title: SATU2_190_S29_R1_001


title: SATU4_197_S40_R1_001


title: SATU4_198_S39_R1_001


title: SATU4_192_S13_R1_001


title: SATU5_199-5_S26_R1_001


title: SATU5_194-5_S28_R1_001


title: SATU5_29-4_S8_R1_001


title: SATU4_191_S31_R1_001


title: SATU2_196_S34_R1_001


title: SATU4_188_S14_R1_001


title: SATU4_189_S35_R1_001


title: SATU2_181_S13_R1_001


title: SATU3_187_S21_R1_001


title: SATU4_201_S38_R1_001


title: SATU1_179_S2_R1_001


title: SATU4_182_S22_R1_001


title: SATU1_183_S26_R1_001


title: SATU4_184_S2_R1_001


title: SATU2_186_S27_R1_001


title: SATU4_177_S32_R1_001


title: SATU1_175_S38_R1_001


title: SATU3_176_S25_R1_001


title: SATU1_185_S20_R1_001


title: SATU3_172_S37_R1_001


title: SATU3_174_S24_R1_001


title: SATU2_178_S17_R1_001


title: SATU5_193-5_S29_R1_001


title: SATU1_173_S34_R1_001


title: SATU3_171_S26_R1_001


title: SATU3_170_S33_R1_001


title: SATU2_169_S14_R1_001


title: SATU4_166_S5_R1_001


title: SATU1_164_S8_R1_001


title: SATU2_165_S9_R1_001


title: SATU5_168-5_S31_R1_001


title: SATU4_162_S28_R1_001


title: SATU4_163_S36_R1_001


title: SATU1_155_S13_R1_001


title: SATU5_158-5_S19_R1_001


title: SATU4_149_S24_R1_001


title: SATU2_150_S28_R1_001


title: SATU5_153-5_S20_R1_001


title: SATU5_160-5_S17_R1_001


title: SATU3_145_S29_R1_001


title: SATU5_147-5_S22_R1_001


title: SATU4_146_S3_R1_001


title: SATU2_143_S35_R1_001


title: SATU3_148_S28_R1_001


title: SATU5_138-4_S23_R1_001


title: SATU4_137_S16_R1_001


title: SATU4_141_S29_R1_001


title: SATU1_139_S9_R1_001


title: SATU3_140_S31_R1_001


title: SATU4_167_S27_R1_001


title: SATU5_135_S24_R1_001


title: SATU3_161_S27_R1_001


title: SATU5_159-4_S18_R1_001


title: SATU2_134_S15_R1_001


title: SATU4_157_S23_R1_001


title: SATU5_132-5_S9_R1_001


title: SATU1_133_S32_R1_001


title: SATU3_131_S9_R1_001


title: SATU2_142_S39_R1_001


title: SATU3_130_S22_R1_001


title: SATU3_128_S35_R1_001


title: SATU4_129_S9_R1_001


title: SATU3_126_S14_R1_001


title: SATU3_127_S30_R1_001


title: SATU3_124_S15_R1_001


title: SATU3_119_S39_R1_001


title: SATU5_123-5_S10_R1_001


title: SATU4_120_S18_R1_001


title: SATU1_136_S21_R1_001


title: SATU2_118_S18_R1_001


title: SATU3_121_S32_R1_001


title: SATU2_125_S33_R1_001


title: SATU1_115_S28_R1_001


title: SATU1_114_S15_R1_001


title: SATU3_117_S10_R1_001


title: SATU3_111_S1_R1_001


title: SATU4_112_S10_R1_001


title: SATU3_113_S16_R1_001


title: SATU3_110_S11_R1_001


title: SATU2_109_S31_R1_001


title: SATU5_108-4_S11_R1_001


title: SATU3_107_S12_R1_001


title: SATU1_106_S17_R1_001


title: SATU4_104_S30_R1_001


title: SATU1_103_S22_R1_001


title: SATU5_101-5_S13_R1_001


title: SATU3_100_S40_R1_001


title: SATU4_102_S25_R1_001


title: SATU4_122_S17_R1_001


title: Adipo-4h-DHA-a

city: Stanford

middle: K

last: Jackson

state: CA

address: 279 Campus Dr., CCSR 3230

institute: Stanford University

data_processing:
BCL files were demultiplexed using bcl2fastq (Illumina), adapters were trimmed using cutadapt and reads were aligned to the mouse genome (mm9) using bowtie2. Duplicates were removed using Picard MarkDuplicates. Mitochondrial reads and reads mapping to a modified version of the mm9 ENCODE blacklist (Table S5) were removed using samtools. Peaks were called using MACS2 and filtered by q value for the top 100K peaks. The peak set was then reduced to non-overlapping peaks and peak width was adjusted to 500 bp.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delim text file

source_name: 3T3L1 cells

growth_protocol: 3T3-L1 cells were grown to confluency in DMEM containing 10% Bovine Calf Serum, followed by another 2 days at confluency in DMEM containing 10% Bovine Calf Serum.

extract_protocol: 200 U/ml DNase (Worthington Biochemical, NJ, USA) were added to the cell aliquot and incubated at 37C for 30 min, centrifuged at 500 g for 5 min at room temperature and resuspended in 1 ml cold PBS. Resuspended samples were centrifuged at 500 g for 5 min at 4C and washed in 500 µl cold RSB buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2) followed by centrifugation at 500 g for 5 min at 4C. Samples were resuspended and lysed for 3 min on ice in 50 µl RSB buffer containing 0.01% Digitonin (Promega, WI, USA), 0.1% NP40 and 0.1% Tween20. After lysis, 950 µl RSB with 0.1% Tween20 were added to the sample and mixed by inverting. Samples were centrifuged at 500 g for 5 min at 4C, resuspended in 50 µl of transposition mix (25 µl TD buffer [Illumina], 2.5 µl Tn5 [Illumina], 16.5 µl PBS, 0.5 µl 1% Digitonin, 0.5 µl 10% Tween20 and 5 µl water) and incubated at 300 rpm at 37C. All samples were purified using MinElute PCR Purification columns (Qiagen, Germany) and amplified and barcoded as previously described (Buenrostro et al., 2015). ATAC libraries were paired-end sequenced (2x 76 bp) on a NextSeq500 (Illumina) using a high output v2 150 cycle kit (Illumina).

treatment_protocol: Adipogenesis was then induced using DMEM containing 10% FBS and either dexamethasone (1 microM) or DHA (100 microM)

value: 3T3L1 cells


title: C6: YDOV-151

city: Seoul

first: Jae-Hoon

address: 211, Eonju-ro, Gangnam-gu

department: Department of Obstetrics and Gynecology

country: South Korea

institute: Gangnam Severance Hospital

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using BeadStudio programme

source_name: Ascites

label_protocol: Biotinylated cRNA were prepared with Illumina Amplification Kit ( Ambion, Inc., San Diego, CA)

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: Ascites

value: Ovarian Cancer


title: Adipo-4h-Dex-b


title: Adipo-4h-DHA-b


title: C2-2: YDOV-157


title: C5: YDOV-105

description: replicate 1

source_name: Ovary

value: Ovary


title: Adipo-0h-b


title: C3-1: YDOV-161

description: replicate 1


title: Adipo-0h-a


title: Adipo-4h-Dex-a


title: C3-2: YDOV-161


title: N3-2: HOSE211

value: normal


title: C2-1: YDOV-157

description: replicate 1


title: N3-1: HOSE211

description: replicate 1


title: C1-2: YDOV-139


title: N2-2: HOSE209


title: C1-1: YDOV-139

description: replicate 1


title: N1-2: HOSE198


title: N2-1: HOSE209

description: replicate 1


title: N1-1: HOSE198

description: replicate 1


title: C4: YDOV-13

description: replicate 1


title: MCF and T3H9 + Prame

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

institute: University Hospital Würzburg

hyb_protocol: Microarray hybridization was performed using the Affymetrix Fluidics Station 450 with program FS450_0001.

scan_protocol: Microarrays were scanned using an Affymetrix GeneChip Scanner 3000 7G.

data_processing: Data preprocessing was performed in R version 3.2.1 using the Bioconductor package oligo version 1.32.0; background correction, normalization and expression value calculation were performed with the rma command using default parameter settings.

source_name: MCF and T-3H9 co-culture in presence of Prame peptide

label_protocol: Total RNA from each sample was processed with the WT PLUS reagent kit (Affymetrix, Santa Clara, CA) following the manufacturer's protocol.

growth_protocol: Cells were cultured in complete RPMI with 10% FCS, penicillin (100 IU/ml), streptomycin (100 IU/ml) and 0.02% sodium pyruvate solution (Gibco, Karlsruhe, Germany) at 37°C and 5% CO2.

extract_protocol: Total RNA was extracted using the TRIZOL reagent.

treatment_protocol: MCF cells were co-cultured with Steap-reactive T3H9 cells in the presence of either the Prame or the Steap peptide.

value: breast cancer cell line

value: T3H9 cells coculture + Prame peptide


title: MCF + Steap

source_name: MCF cells cultured in presence of Steap peptide

value: Steap peptide


title: MCF and T3H9 + Steap

source_name: MCF and T-3H9 co-culture in presence of Steap peptide

value: T3H9 cells coculture + Steap peptide


title: N4: HOSE213

description: replicate 1


title: Activated gametocyte untreated (G9a) 1 h

city: University Park

first: Manuel

last: Llinas

state: Pennsylvania

address: Millennium Science Complex, Pollock Rd

department: Biochemistry and Molecular Biology

institute: Penn State University

hyb_protocol: Painter, H. J., Altenhofen, L. M., Kafsack, B. F. C. & Llinás, M. Whole-genome analysis of Plasmodium spp. Utilizing a new agilent technologies DNA microarray platform. Methods Mol. Biol. 923, 213–219 (2013).

scan_protocol: Agilent G2600D Microarray Scanner. Images were quantified using Agilent Feature Extraction Software (version 11.5.1.1).

data_processing: Agilent Feature Extraction Software (v 11.5.1.1) was used for background subtraction.

organism: Plasmodium falciparum

source_name: Activated gametocyte RNA

growth_protocol: P. falciparum NF54 strain were cultivated in vitro in RPMI 1640 medium supplemented with 10% heat-inactivated human serum [50] and cultures were maintained at 37°C in nitrogen containing  5% O2 and 5% CO2. Cultures were synchronized by repeated sorbitol treatment as described [51]. To generate gametocytes, the cultures were kept at high parasitaemia and gametocytogenesis was induced following addition of lysed RBCs. As soon as stage I gametocytes emerged  in the culture, the culture medium was supplemented with 50 mM N-acetyl glucosamine (GlcNac) for approximately 5 days to kill the asexual blood stages [52]. The gametocyte culture was then maintained in normal culture medium without GlcNac until immature (stage II -IV) or mature stage V gametocytes were harvested and enriched by Percoll gradient centrifugation [53]. In order to obtain activated gametocytes, Percoll enriched mature gametocytes were incubated with 100 µM XA (Xanthurenic acid) 1 h or 6 h at room temperature (RT).

extract_protocol: Gametocytes samples were purified from different cultures, treated as indicated and stored in Trizol at –80°C. Samples treated in the same way were then pooled together and total RNA extracted according to the manufacturer´s instructions (Invitrogen).

treatment_protocol: P. falciparum Percoll enriched immature (stages II-IV) gametocytes (imGC), mature (stage V) gametocytes (mGC), and gametocytes at 1 h post-activation with 100 µM Xanthurenic acid at RT (aGC) were obtained. Each enriched gametocyte sample was treated with BIX-01294 at IC90 concentrations (0.12 µM) or with 0.5% vol. DMSO (untreated control) for 1 h and 6 h.

tag: strain

value: NF54 Wildtype

source_name: Mixed gametocyte and asexual blood stage reference pool

value: NF54 and 3D7


title: Activated gametocyte BIX-treated (G9a) 1 h

label_protocol: Painter, H. J., Altenhofen, L. M., Kafsack, B. F. C. & Llinás, M. Whole-genome analysis of Plasmodium spp. Utilizing a new agilent technologies DNA microarray platform. Methods Mol. Biol. 923, 213–219 (2013).


title: Activated gametocyte BIX-treated (G9a) 6 h


title: 497B_DH [Bisulfite-seq]

first: Lisa

last: Goldberg

address: 130 Biobehavioral Health Bldg, Penn State University

department: Biobehavioral Health

description: Bisulfite-converted DNA

data_processing:
FASTQ files were quality checked via FASTQC. Illumina adapter sequences were removed and low-quality bases were trimmed using Trimmomatic.
Trimmed reads were mapped to the mouse reference genome (mm10) using Bowtie2 implemented in Bismark.
Methyl_extract within Bismark was used to extract CpG methylation information and to create methylation reports.
MethylKit was used for analysis of differentially methylated regions (DMRs).
Methylation status was summarized over non-overlapping windows of 500 base pairs and differential methylation analysis was performed.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *pe.bismark.cov: Bismark methylation reports.

source_name: Dorsal hippocampus

extract_protocol:
Dorsal and ventral hippocampal were removed, flash frozen on dry ice, and DNA was harvested using an AllPrep DNA/RNA mini kit (Qiagen).
Libraries were constructed using the KAPA Hyper Prep kit (Kapa Biosystems). Sodium bisulfite converted libraries were PCR amplified and enriched for selected genomic regions using a custom capture probe set (SeqCap Epi Choice Probes; Roche).

tag: strain/background

value: Male

value: Dorsal hippocampus

tag: paternal treatment

value: Saline


title: 499A_DH [Bisulfite-seq]

description: Bisulfite-converted DNA

value: Female


title: 497C_DH [Bisulfite-seq]

description: Bisulfite-converted DNA


title: 499C_VH [Bisulfite-seq]

description: Bisulfite-converted DNA

source_name: Ventral hippocampus

value: Ventral hippocampus


title: 497C_VH [Bisulfite-seq]

description: Bisulfite-converted DNA


title: 499B_DH [Bisulfite-seq]

description: Bisulfite-converted DNA


title: 499C_DH [Bisulfite-seq]

description: Bisulfite-converted DNA


title: 499A_VH [Bisulfite-seq]

description: Bisulfite-converted DNA


title: 497A_DH [Bisulfite-seq]

description: Bisulfite-converted DNA


title: 497A_VH [Bisulfite-seq]

description: Bisulfite-converted DNA


title: Mature gametocytes BIX-treated (G9a) 6 h

source_name: Mature gametocyte RNA


title: Activated gametocyte untreated (G9a) 6 h


title: 493C_VH [Bisulfite-seq]

description: Bisulfite-converted DNA

value: Nicotine


title: Immature gametocytes untreated (G9a) 1 h

source_name: Immature gametocyte RNA


title: Mature gametocytes untreated (G9a) 6 h


title: Immature gametocytes BIX-treated (G9a) 6 h


title: Immature gametocytes BIX-treated (G9a) 1 h


title: 499B_VH [Bisulfite-seq]

description: Bisulfite-converted DNA


title: 493C_DH [Bisulfite-seq]

description: Bisulfite-converted DNA


title: 497B_VH [Bisulfite-seq]

description: Bisulfite-converted DNA


title: Mature gametocytes untreated (G9a) 1 h


title: Mature gametocytes BIX-treated (G9a) 1 h


title: Immature gametocytes untreated (G9a) 6 h


title: 493B_VH [Bisulfite-seq]

description: Bisulfite-converted DNA


title: 493B_DH [Bisulfite-seq]

description: Bisulfite-converted DNA


title: 493A_VH [Bisulfite-seq]

description: Bisulfite-converted DNA


title: 493A_DH [Bisulfite-seq]

description: Bisulfite-converted DNA


title: 492C_DH [Bisulfite-seq]

description: Bisulfite-converted DNA


title: 492C_VH [Bisulfite-seq]

description: Bisulfite-converted DNA


title: 499C_DH [RNA-seq]

description: processed data file: counts.txt

data_processing:
FASTQ files were aligned to a mouse reference genome using TopHat (v2.1.0) on Galaxy Project.
Cufflinks and Cuffmerge (v2.2.1.0) were used to assemble transcripts from mapped reads and merge transcript files for final transcriptome assembly.
False discovery rate (FDR) adjusted p-values were computed for differential gene expression from NIC-Sired and SAL-Sired samples using Cuffdiff (v2.2.1.3).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: counts.txt: Tab-delimited text file includes counts for all samples.

extract_protocol:
Dorsal and ventral hippocampal were removed, flash frozen on dry ice, and RNA was harvested using an AllPrep DNA/RNA mini kit (Qiagen).
Illumina TruSeq Stranded mRNA Library prep kit was used for the construction of sequencing libraries (150 bp single-end reads).
Samples were sequenced using the Illumina HiSeq2500 over 3 lanes (L1, L2, L3).


title: 499B_DH [RNA-seq]

description: processed data file: counts.txt


title: 492A_VH [Bisulfite-seq]

description: Bisulfite-converted DNA


title: 492B_VH [Bisulfite-seq]

description: Bisulfite-converted DNA


title: 499C_VH [RNA-seq]

description: processed data file: counts.txt


title: 499B_VH [RNA-seq]

description: processed data file: counts.txt


title: 499A_VH [RNA-seq]

description: processed data file: counts.txt


title: 492B_DH [Bisulfite-seq]

description: Bisulfite-converted DNA


title: 497C_VH [RNA-seq]

description: processed data file: counts.txt


title: 497C_DH [RNA-seq]

description: processed data file: counts.txt


title: 497B_VH [RNA-seq]

description: processed data file: counts.txt


title: 499A_DH [RNA-seq]

description: processed data file: counts.txt


title: 497B_DH [RNA-seq]

description: processed data file: counts.txt


title: 497A_VH [RNA-seq]

description: processed data file: counts.txt


title: Ecoli_rne_T5_kinetic2

city: Toulouse

first: Laurence

last: Girbal

address: 135 avenue de rangueil

country: France

institute: TBI

description:
Escherichia coli MG1662
Cells were in mid-exponential phase, the sampling was performed 5 minutes after rifampicin addition. It is the second kinetics out of 3 for this strain.

hyb_protocol: According to manufacturer instructions, 2 µg of labeled cDNA were hybridized onto E. coli K-12 gene expression arrays (Nimblegen, Roche) during 17 h at 42 °C.

scan_protocol: Arrays were later washed and scanned using MS200 Microarray Scanner (Nimblegen, Roche). Pictures were analyzed with DEVA 1.2.1 software.

data_processing:
Raw probe intensities ( .pair files three replicates for each strain before and after transcription arrest by rifampicin addition) were processed and analyzed with R computing environment using the affy and limma package of Bioconductor. Twelve arrays (three reference T0 samples, and nine time points after addition of rifampicin) were used. Only a normalization between arrays according to an invariant probeset intensities was performed. For each strain, a set of probes in the background for which the ranks were roughly invariant across all twelve arrays was selected. The median value of the invariant probe set intensities in each condition was used as a scaling factor for normalization between the three strains. After normalization, the intensity of a transcript was calculated by a RMA-summarization procedure [Irizarry et al, 2003, Biostatistics 4(2): 249-264] within each condition.
After normalization, in each array, transcript-specific intensity was computed as the median value of the 16 targeting probe intensities.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli, rne, Sampling 5 minutes after rifampicin addition in kinetic 2

label_protocol: According to manufacturer instructions, 1 µg of cDNA was labeled using one color DNA labeling kit.

growth_protocol: The laboratory strain E. coli K12 MG1655 referred as the rne+ strain and its mutant strain E. coli rne (ΔMTS) were grown in bioreactors in M9 glucose (3g/l) at 37 °C. The pH was set to 7. All cultures were inoculated at OD 0.1 from overnight pre-cultures performed in similar conditions. Biomass was estimated from absorbance at 600 nm. Each culture was repeated three times to provide independent biological kinetics.

extract_protocol: After thawing and centrifugation steps, total RNA was extracted with TRIZOL® Reagent (Ambion) according to the manufacturer’s instructions. DNA contamination was eliminated with Turbo DNase kit (Ambion). Total RNA concentration and integrity were measured using a Nanodrop® spectrophotometer and Agilent BioAnalyzer, respectively.

treatment_protocol: In mid-exponential phase, samples were collected for the reference time point (T0) for the half-life determination procedure. Subsequently, rifampicin (500 µg.mL-1) was added to inhibit the initiation of transcription, and cells were harvested at three different time points after this addition. Cultures were performed in triplicate. Samples were immediately frozen in liquid nitrogen upon collection.

tag: genotype/variation

value: rne+

value: rifampicin

tag: sampling time

value: 5 minutes after rifampicin addition

tag: repetition

value: kinetic 2


title: 497A_DH [RNA-seq]

description: processed data file: counts.txt


title: Ecoli_rne_T1min30sec_kinetic3

description:
Escherichia coli MG1664
Cells were in mid-exponential phase, the sampling was performed 1 minute et 30 seconds after rifampicin addition. It is the third kinetics out of 3 for this strain.

source_name: E. coli, rne, Sampling 1 minute and 30 seconds after rifampicin addition in kinetic 3

value: kinetic 3


title: Ecoli_rne_T3_kinetic3

description:
Escherichia coli MG1665
Cells were in mid-exponential phase, the sampling was performed 3 minutes after rifampicin addition. It is the third kinetics out of 3 for this strain.

source_name: E. coli, rne, Sampling 3 minutes after rifampicin addition in kinetic 3

value: 3 minutes after rifampicin addition


title: 492A_DH [Bisulfite-seq]

description: Bisulfite-converted DNA


title: Ecoli_rne_T7_kinetic3

description:
Escherichia coli MG1666
Cells were in mid-exponential phase, the sampling was performed 7 minutes after rifampicin addition. It is the third kinetics out of 3 for this strain.

source_name: E. coli, rne, Sampling 7 minutes after rifampicin addition in kinetic 3

value: 7 minutes after rifampicin addition


title: Ecoli_rne_T0_kinetic3

description:
Escherichia coli MG1663
Cells were in mid-exponential phase, the sampling was performed just before rifampicin addition. It is the third kinetics out of 3 for this strain.

source_name: E. coli, rne, Sampling before rifampicin addition in kinetic 3

value: before rifampicin addition


title: Ecoli_rne_T2min30sec_kinetic2

description:
Escherichia coli MG1661
Cells were in mid-exponential phase, the sampling was performed 2 minutes et 30 seconds after rifampicin addition. It is the second kinetics out of 3 for this strain.

source_name: E. coli, rne, Sampling 2 minutes and 30 seconds after rifampicin addition in kinetic 2


title: Ecoli_rne_T30sec_kinetic1

description:
Escherichia coli MG1656
Cells were in mid-exponential phase, the sampling was performed 30 seconds after rifampicin addition. It is the first kinetics out of 3 for this strain.

source_name: E. coli, rne, Sampling 30 seconds after rifampicin addition in kinetic 1

value: 30 seconds after rifampicin addition

value: kinetic 1


title: Ecoli_rne_T1_kinetic2

description:
Escherichia coli MG1660
Cells were in mid-exponential phase, the sampling was performed 1 minute after rifampicin addition. It is the second kinetics out of 3 for this strain.

source_name: E. coli, rne, Sampling 1 minute after rifampicin addition in kinetic 2

value: 1 minute after rifampicin addition


title: Ecoli_rne_T2_kinetic1

description:
Escherichia coli MG1657
Cells were in mid-exponential phase, the sampling was performed 2 minutes after rifampicin addition. It is the first kinetics out of 3 for this strain.

source_name: E. coli, rne, Sampling 2 minutes after rifampicin addition in kinetic 1

value: 2 minutes after rifampicin addition


title: Ecoli_rne_T0_kinetic1

description:
Escherichia coli MG1655
Cells were in mid-exponential phase, the sampling was performed just before rifampicin addition. It is the first kinetics out of 3 for this strain.

source_name: E. coli, rne, Sampling before rifampicin addition in kinetic 1


title: 493C_VH [RNA-seq]

description: processed data file: counts.txt


title: 493C_DH [RNA-seq]

description: processed data file: counts.txt

value: Dorsal hippocampus


title: Ecoli_rne_T4_kinetic1

description:
Escherichia coli MG1658
Cells were in mid-exponential phase, the sampling was performed 4 minutes after rifampicin addition. It is the first kinetics out of 3 for this strain.

source_name: E. coli, rne, Sampling 4 minutes after rifampicin addition in kinetic 1

value: 4 minutes after rifampicin addition


title: 493B_VH [RNA-seq]

description: processed data file: counts.txt

value: Female


title: 493A_VH [RNA-seq]

description: processed data file: counts.txt

value: Ventral hippocampus


title: 493A_DH [RNA-seq]

description: processed data file: counts.txt

value: Nicotine


title: 493B_DH [RNA-seq]

description: processed data file: counts.txt


title: 492C_VH [RNA-seq]

description: processed data file: counts.txt

value: Male


title: 492C_DH [RNA-seq]

description: processed data file: counts.txt


title: Ecoli_rne_T0_kinetic2

description:
Escherichia coli MG1659
Cells were in mid-exponential phase, the sampling was performed just before rifampicin addition. It is the second kinetics out of 3 for this strain.

source_name: E. coli, rne, Sampling before rifampicin addition in kinetic 2

value: rne+


title: 492B_DH [RNA-seq]

description: processed data file: counts.txt


title: 492B_VH [RNA-seq]

description: processed data file: counts.txt


title: 492A_VH [RNA-seq]

description: processed data file: counts.txt


title: 492A_DH [RNA-seq]

description: processed data file: counts.txt


title: mouse whole spleen saline control replicate 1

city: South San Francisco

first: Nimrod

middle: Daniel

last: Rubinstein

address: 1170 Veterans blvd

institute: Calico

data_processing:
Single-cell fastq files were demultiplexed to their respective barcodes using the 10X Genomics Cell Ranger mkfastq utility
Unique Molecular Identifier (UMI) counts were generated for each barcode using the Cell Ranger count utility using the mm10 reference genome and the mouse Gencode version M12 annotation  for mouse and HetGla2.0 reference genome along with the RefSeq GCF_000247695.1 annotation for naked mole-rat
For each single-cell sample barcodes that were not likely to represent captured cells were filtered out by detecting the first local minimum above 2 in a distribution of log10(#UMIs).
For each single-cell sample genes that are too sparsely captured across barcodes were filtered out by detecting the first local minimum above 3 in a distribution of log10(#barcodes)
For each single-cell sample barcodes capturing more than a single cell (multiplets) were sought as local modes in the distributions of log10(#genes) and log10(#UMIs), whose x-axis maxima are more than 1.5 higher than that of the x-axis location of the global maximum of the respective distribution and includes less than 5% of the total number of barcodes
Whole spleen RNA read data were mapped using STAR aligner version 2.5.3a
Transcript and gene abundances of whole spleen mapped RNA read data were quantified using MMSEQ
Genome_build: For mouse: mm10 reference genome and the mouse Gencode version M12 annotation. For naked mole-rat the HetGla2.0 reference genome and the RefSeq GCF_000247695.1 annotation for naked mole-rat
Supplementary_files_format_and_content: For the single-cell data processed data files are comma separated matrices of UMI counts where rows are gene IDs (Ensembl for mouse and Entrez for naked mole-rat) and columns are barcodes. The genes and barcode that are included are those that were retained following all filtering steps

source_name: whole spleen

extract_protocol:
1ml TRIzol reagent (4C) (Invitrogen, 15596026) added to 20mg frozen splenic tissue in a 2ml microcentrifuge tube along with a single stainless-steel bead (Qiagen, 69965) and homogenization was performed using a Tissuelyser II (Qiagen) (30Hz for 2mins)
Illumina TruSeq Stranded Total RNA kit paired with the Ribo-Zero rRNA removal kit
Single cells were extracted using 10X Genomics Chromium Controller droplet emulsion capture. Whole tissue RNA was purified using 1ml TRIzol reagent (4C) (Invitrogen, 15596026) added to 20mg frozen splenic tissue in a 2ml microcentrifuge tube along with a single stainless-steel bead (Qiagen, 69965) and homogenization was performed using a Tissuelyser II (Qiagen) (30Hz for 2mins)
Single cell libraries were contructed using 10X Genomics Chromium Single-Cell 3’ Gel Bead and Library V2 Kit, suspending cells in PBS with 5% FBS to a final concentration of 1 x 10^6 cells/ml (1000 cells per ul) and loaded in each channel with a target output of 3000 cells. Reactions performed with Bio-Rad C100 Touch Thermal Cycler with a 96 Deep Well Reaction Module, 12 cycles for cDNA amplificationand OCR indexing. Whole spleen RNA libraries were contructed using Illumina TruSeq Stranded Total RNA kit paired with the Ribo-Zero rRNA removal kit

treatment_protocol: all animals were anasthesiasized with isoflurane. Saline controls received an intraperitoneal 200µl sterile saline injection. LPS-chllaneged animals received an intraperitoneal 1mg/kg lipopolysaccharide injection

value: whole spleen

tag: condition

value: saline control

value: male

tag: age

value: 8-10 weeks old


title: mouse whole spleen saline control replicate 2

value: female


title: mouse whole spleen LPS-challenged replicate 1

value: LPS challenge


title: mouse circulating immune cells LPS-challenged sample 2 replicate 1

source_name: single circulating immune cells

extract_protocol:
10X Genomics Chromium Controller droplet emulsion capture
10X Genomics Chromium Single-Cell 3’ Gel Bead and Library V2 Kit, suspending cells in PBS with 5% FBS to a final concentration of 1 x 10^6 cells/ml (1000 cells per ul) and loaded in each channel with a target output of 3000 cells. Reactions performed with Bio-Rad C100 Touch Thermal Cycler with a 96 Deep Well Reaction Module, 12 cycles for cDNA amplificationand OCR indexing
Single cells were extracted using 10X Genomics Chromium Controller droplet emulsion capture. Whole tissue RNA was purified using 1ml TRIzol reagent (4C) (Invitrogen, 15596026) added to 20mg frozen splenic tissue in a 2ml microcentrifuge tube along with a single stainless-steel bead (Qiagen, 69965) and homogenization was performed using a Tissuelyser II (Qiagen) (30Hz for 2mins)
Single cell libraries were contructed using 10X Genomics Chromium Single-Cell 3’ Gel Bead and Library V2 Kit, suspending cells in PBS with 5% FBS to a final concentration of 1 x 10^6 cells/ml (1000 cells per ul) and loaded in each channel with a target output of 3000 cells. Reactions performed with Bio-Rad C100 Touch Thermal Cycler with a 96 Deep Well Reaction Module, 12 cycles for cDNA amplificationand OCR indexing. Whole spleen RNA libraries were contructed using Illumina TruSeq Stranded Total RNA kit paired with the Ribo-Zero rRNA removal kit

value: single circulating immune cells


title: mouse circulating immune cells saline control sample 2 replicate 1


title: mouse circulating immune cells LPS-challenged sample 1 replicate 1


title: PC-LPS-KO-14M

city: Cambridge

first: Stefka

last: Gyoneva

state: MA

address: 225 Binney St.

institute: Biogen, Inc

data_processing:
Raw reads were aligned to mouse genome build mm10 using STAR version 2.5.2a and transcripts quantified with RSEM version 1.2.26
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text; gene level count table - *_genes.estcount_table.txt; gene level FPKM table - *_genes.fpkm_table.txt; gene level TPM table - *_genes.tpm_table.txt

source_name: Peritoneal cells

growth_protocol: All mice used in the current manuscript are littermate controls derived from Cx3cr1+/eGFP crosses. The mice were maintained on a normal diet in a 12-hour light/dark cycle. Approximately five mice were used per group (per sex, age, genotype and treatment).

extract_protocol:
Brains were finely minced with a razor blade and tissues were dissociated to single cell suspension with Accutase on ice for 30 min. Cell suspensins were resuspended with 33% Percoll and centrifuged for 15 min at 800g (no brake). Cells were washed, stained and subjected to sorting for CD11b(+)CD45(lo) cells. RNA was isolated from sorted microglia using Qiagen Universal AllPrep kit (Qiagen 80004) according to the manufacturer’s instructions.
cDNA for RNA-Seq libraries was prepared using 10 ng of RNA using the SmartSeq v4 Ultra Low RNA Input Library prep protocol (Clontech 634889) according to the manufacturer’s instruction.
The cDNA (250 ng starting material) was then tagged and fragmented with the NexteraXT DNA Library Preparation kit (Illumina FC-131-1024) according to the manufacturer’s instructions. Quality of amplified cDNA and fragmented libraries was assessed on a Bioanalyzer with the High Sensitivity DNA chips (Agilent 5067-4627). Tagged libraries were pooled (8 nM total DNA) and sequenced on an Illumina HiSeq2500 sequencer, with target depth of 20 million of 50 bp paired end reads

treatment_protocol: Mice were deeply anesthetized with 10 mg/kg ketamine, 30 mg/kg xylazine until they failed to respond to toe pinch and transcardially perfused with cold phosphate-buffered saline (PBS). Mice for the LPS study were euthanized by CO2 asphyxiation, peritoneal cells were isolated by flushing the peritoneal cavity with cold PBS, and then perfused. In all cases, the brain was then isolated and stored in PBS on ice until processing.

tag: cx3cr1 genotype

value: KO

value: 2 months

value: M

value: Peritoneal cells

value: LPS


title: mouse circulating immune cells saline control sample 1 replicate 2


title: mouse whole spleen LPS-challenged replicate 2


title: CvCa_SKG-I_siIGF2R_rep2

city: Tokyo

first: Masayuki

last: Komatsu

address: 5-1-1, Tsukiji, Chuo-ku

institute: National Cancer Center Research Institute

description: IGF2R siRNA-expressing cells

hyb_protocol: Following fragmentation, 10µg of cRNA were hybridized for 16 hr at 45ﾟC on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

data_processing: The data were analyzed with GeneSpring version 14.9 using affymetrix expression analysis settings (Summarization algorithm: MAS5).

source_name: Cervical cancer cell line

label_protocol: Biotinylated cRNA were prepared from 100 ng total RNA by GeneChip 3' IVT Express Kit. The procedure was according to the standard Affymetrix protocol.

growth_protocol: Cells were maintained in 10% FBS-containing Ham's F12 medium under an atmosphere of 5% CO2 and 95% air at 37˚C.

extract_protocol: Cultured cells were washed by D-PBS and lysed by ISOGEN solution. Extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cell were subjected to DharmaFECT-based lipofection of control or IGF2R siRNA according to the manufacturer's instructions and then cultured for 72 hours.

tag: cell line

value: SKG-I


title: PC-LPS-KO-13F

value: F

tag: cell type

tag: treatment


title: CvCa_BOKU_siIGF2R_rep1

description: IGF2R siRNA-expressing cells

value: BOKU


title: CvCa_SKG-I_siCtrl_rep2

description: Control siRNA-expressing cells


title: PC-LPS-KO-12F


title: mouse circulating immune cells LPS-challenged sample 2 replicate 2

tag: tissue


title: CvCa_SKG-I_siCtrl_rep1

description: Control siRNA-expressing cells


title: CvCa_SKG-I_siIGF2R_rep1

description: IGF2R siRNA-expressing cells


title: CvCa_BOKU_siIGF2R_rep2

description: IGF2R siRNA-expressing cells


title: CvCa_BOKU_siCtrl_rep2

description: Control siRNA-expressing cells


title: CvCa_BOKU_siCtrl_rep1

description: Control siRNA-expressing cells


title: Project08_single cells

city: Minneapolis

first: Zohar

last: Sachs

state: MN

address: 420 Delaware Street SE MMC 480

department: Department of Medicine, Division of Hematology, Oncology and Transplantation

institute: University of Minnesota Twin Cities

description: 106(forward and reverse) fastq files for 53 single cell data

data_processing:
FastQC is run on each fastq file to generate sequence quality plots. Sequence adaptors and low-quality sequence were removed using Trimmomatic (v0.32). Trimmed reads were mapped with TOPHAT 2.0 (v2.0.10) to the mouse reference genome (UCSC GRCm38/mm10 assembly). An additional chromosome was added to the reference genome that contained the transgenes that were expressed in the mouse model (NRASG12V, MLL-AF9 and EGFP)1. Insertion size metrics were calculated for each sample using Picard software (version 1.126). Samtools software (version 1.0_BCFTools_HTSLib)2 was used to sort and index the bam files.  Cuffquant (Cufflinks version 2.2.1)3 was used to generate transcript abundance files (options used include the multi-read-correct). Murine cells with less than 75% alignment to the genome were omitted from further analysis. Each cell expressed a minimum of 1,300 genes. There were 42, 33, and 51 evaluable cells in the discovery data set, validation dataset, and Ras-off dataset, respectively. Human cells were analyzed to omit outliers per SINGuLAR Analysis Toolkit (Fluidigm). This approach identifies cells whose expression of the most commonly expressed genes exceeds the 15th percentile; cells that meet this criterion are included in the analysis, the remaining cells are omitted as outliers. In the human dataset, 25 cells were included in the analysis. After mapping and abundance estimates were completed, Cuffnorm (Cufflinks version 2.2.1)3 was used to generate fragments per kilobase of transcript per million mapped reads (FPKM) values.
Genome_build: mm10 and GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each single cell sample or bulk RNA

source_name: spleen

extract_protocol:
Primary murine NRASG12V/Mll-AF9 AMLs were harvested from spleens of leukemic mice, stained with antibodies for cell surface markers, and sorted on a FACAria (Becton Dickinson, Franklin Lakes, NJ). Cryopreserved bone marrow aspirates from healthy volunteers were purchased from Lonza (Basel, Switzerland). AML samples with >50% bone marrow blasts were obtained from the University of Minnesota Hematological Malignancies Tissue Bank in accordance with the University of Minnesota Institutional Review Board (IRB #1506E72802 and #0611M96846).Fresh AML bone marrow aspirates were CD34-selected using EasySep Magnet and EasySep Human CD34 antibody kit (StemCell Technologies, Vancouver, BC, Canada). Human AML and normal bone marrow were sorted to isolate CD34+CD38- cells. Sorted or magnet-selected cells were stained with a Live/Dead Viability and Cytotoxicity dye (Life Technologies, Carlsbad, California, # L-3224) and loaded at 250 cells/l for single-cell capture on the C1 Single-Cell Auto Prep Integrated Fluidic Circuit for small cells (5-10 m, Fluidigm, South San Francisco, California).
Captured cells were imaged to identify single, live cells for cDNA preparation. SMARTer Ultra Low RNA Kit for the Fluidigm C1 System (Takara Bio, Kusatsu, Shiga Prefecture, Japan) was used to prepare cDNA for sequencing. Fluidigm Reverse Transcription Master mix was used to prepare cDNA for PCR.

value: Leukemia stem cells

value: spleen

tag: disease state

value: acute myeloid leukemia (AML)


title: Project05_single cells

description: 100(forward and reverse) fastq files for 49 single cell data


title: PC-LPS-KO-11M


title: mouse circulating immune cells LPS-challenged sample 1 replicate 2


title: Project09_bulk

description: bulk RNA-seq


title: mouse circulating immune cells saline control sample 1 replicate 1

value: saline control


title: Project09_single cells

description: 88(forward and reverse) fastq files for 43 single cell data and 1 bulk data


title: mouse circulating immune cells saline control sample 2 replicate 2


title: PC-LPS-KO-9F


title: PC-LPS-KO-10M


title: mouse spleen LPS-challenged sample 2 replicate 2

source_name: single spleen cells

value: single spleen cells


title: mouse spleen LPS-challenged sample 1 replicate 1

value: male

value: 8-10 weeks old


title: mouse spleen LPS-challenged sample 1 replicate 2

value: LPS challenge


title: PC-LPS-KO-8F


title: PC-LPS-Het-10F

value: Het


title: PC-LPS-Het-9F


title: mouse spleen saline control sample 2 replicate 2

value: female


title: PC-LPS-Het-8M

value: 2 months


title: mouse spleen saline control sample 1 replicate 2


title: mouse spleen saline control sample 1 replicate 1


title: mouse spleen saline control sample 2 replicate 1


title: PC-LPS-Het-5M

value: M


title: PC-LPS-Het-7M

value: Peritoneal cells


title: mouse circulating immune cells sample 2

description: mouse circulating immune cells sample 2

value: single circulating immune cells

value: normal


title: mouse circulating immune cells sample 3

description: mouse circulating immune cells sample 3


title: PC-LPS-WT-11M

value: WT

value: LPS


title: mouse spleen LPS-challenged sample 2 replicate 1


title: mouse circulating immune cells sample 4

description: mouse circulating immune cells sample 4


title: PC-LPS-Het-4M


title: mouse spleen sample 4 replicate 2

description: mouse spleen sample 4 replicate 2


title: PC-LPS-WT-11F

value: F


title: PC-LPS-Het-6F


title: PC-LPS-WT-12F


title: mouse circulating immune cells sample 1

description: mouse circulating immune cells sample 1


title: mouse spleen sample 3 replicate 2

description: mouse spleen sample 3 replicate 2


title: PC-LPS-WT-9M


title: mouse spleen sample 3 replicate 1

description: mouse spleen sample 3 replicate 1


title: PC-LPS-WT-10F


title: PC-LPS-WT-6F


title: mouse spleen sample 4 replicate 1

description: mouse spleen sample 4 replicate 1


title: PC-LPS-WT-8M


title: mouse spleen sample 2 replicate 2

description: mouse spleen sample 2 replicate 2


title: mouse spleen sample 1 replicate 2

description: mouse spleen sample 1 replicate 2


title: mouse spleen sample 2 replicate 1

description: mouse spleen sample 2 replicate 1


title: mouse spleen sample 1 replicate 1

description: mouse spleen sample 1 replicate 1


title: PC-LPS-WT-5F


title: PC-LPS-WT-1M


title: PC-Sal-KO-3F

value: KO

value: Saline


title: CRBT222 [Oligo_cont_32]

city: Lyon

first: Mathilde

last: PARIS

address: 32-34 avenue Tony Garnier

department: Institut de Genomique Fonctionnelle de Lyon

institute: CNRS

description:
processed data file:
est_counts_155cells_CellsRenamed_GeneNames.txt
description_155cells.txt

data_processing:
Reads were processed using Kallisto (Bray et al. Nature Biotechnology 2016) and the mouse genome (ENSEMBL Release GRCm38) with the following parameters : -l 350 -s 50 -b 100.
Gene levels were obtained by summing up TPM or counts over their transcripts.
We selected 155 cells for which at least 20% of the sequenced reads mapped to the annotation, for a total of at least 50000 mapped reads.
We selected 3422 genes that had a raw read count above 10 in at least 5 selected cells.
Gene counts were TMM normalized using the function normalizeBetweenArrays from the R package limma, so that the quantiles of the different samples were identical.
Genome_build: GRCm38)
Supplementary_files_format_and_content: est_counts_155cells_CellsRenamed_GeneNames.txt : tab-delimited text file containing estimted counts for each gene (rows) in each Sample (columns). The names of the genes and cells are given.
Supplementary_files_format_and_content: description_155cells.txt: tab-delimited text file decribing each cell (e.g. cell type)

extract_protocol:
Single-cell suspensions, previously stained with the Fixable Viability Dye eFluor780 (Thermofisher 65-0865-14), were sorted on a 4-laser BD FACS Influx (BD Biosciences) equipped with a 100 µm nozzle. Single live cells were gated based on forward scatter, side scatter, trigger pulse width, and viability dye parameters. Autofluorescent cells were excluded based on their non-specific signal in the Amcyan channel. Cells were further gated as Gad67-GFP+, Olig2-Tomato+, or double positive. Single cells were FACS sorted into 96-well PCR plates containing 3μL lysis buffer (10:1 mix of Resuspension Buffer and Lysis Enhancer from Cells Direct one-step qRT-PCR kit, Thermofisher 11753100)
SMART-Seq2 according to Picelli et al. (2014)

treatment_protocol: NBL, OligNBL and OL single cells were dissociated from dissected SVZ and CC from demyelinated mice (8-10 weeks old, n=5 mice) 6 days after LPC injection, during the peak of cell mobilization in the SVZ. Control NB and O single cells were collected from healthy non-injected mice (8-10 weeks old, n=5 mice)

value: Olig2-tdTomato TH39Gsat/Mmcd

value: brain (sub-ventricular zone and corpus callosum)

tag: lesion state

value: control

value: O

tag: cell population name


title: PC-LPS-Het-3M

tag: Sex


title: CRBT221 [Oligo_cont_31]

tag: strain

value: 8-10 weeks old


title: PC-Sal-KO-2F


title: PC-Sal-KO-1F


title: CRBT220 [Oligo_cont_30]


title: CRBT218 [Oligo_cont_28]


title: CRBT219 [Oligo_cont_29]


title: PC-Sal-WT-4M


title: PC-Sal-WT-2F


title: CRBT217 [Oligo_cont_26]


title: CRBT216 [Oligo_cont_25]


title: PC-Sal-WT-3M


title: PC-Sal-WT-1F


title: MG-LPS-KO-14M

source_name: Microglia

value: Microglia


title: MG-LPS-KO-13F


title: CRBT215 [Oligo_cont_24]


title: MG-LPS-KO-12F


title: CRBT214 [Oligo_cont_23]


title: CRBT213 [Oligo_cont_22]


title: CRBT212 [Oligo_cont_21]


title: CRBT211 [Oligo_cont_20]


title: CRBT210 [Oligo_cont_19]


title: MG-LPS-KO-9F


title: CRBT209 [Oligo_cont_18]


title: MG-LPS-KO-11M


title: CRBT208 [Oligo_cont_17]


title: MG-LPS-KO-10M


title: MG-LPS-Het-10F

value: Het


title: CRBT206 [Oligo_cont_13]


title: MG-LPS-Het-9F

value: 2 months


title: CRBT207 [Oligo_cont_16]


title: MG-LPS-Het-8M

value: M


title: MG-LPS-Het-7M


title: CRBT203 [Oligo_cont_9]


title: MG-LPS-Het-5M


title: CRBT202 [Oligo_cont_8]


title: CRBT201 [Oligo_cont_7]


title: MG-LPS-Het-3M


title: MG-LPS-WT-12F


title: CRBT199 [Oligo_cont_5]


title: CRBT196 [Oligo_cont_2]


title: CRBT197 [Oligo_cont_3]


title: MG-LPS-KO-8F


title: MG-LPS-WT-11F


title: MG-LPS-WT-11M


title: MG-LPS-WT-10F


title: CRBT195 [Oligo_cont_1]


title: CRBT193 [Oligo_les_31]

value: lesion

value: OL


title: MG-LPS-WT-8M


title: MG-LPS-WT-9M


title: CRBT194 [Oligo_les_32]


title: MG-LPS-WT-6F


title: CRBT205 [Oligo_cont_11]


title: MG-LPS-WT-5F


title: CRBT190 [Oligo_les_28]


title: MG-LPS-Het-4M


title: MG-LPS-Het-6F


title: CRBT200 [Oligo_cont_6]


title: CRBT188 [Oligo_les_26]


title: CRBT187 [Oligo_les_25]


title: CRBT198 [Oligo_cont_4]


title: CRBT186 [Oligo_les_24]


title: MG-Sal-KO-2F


title: MG-Sal-KO-1F


title: CRBT185 [Oligo_les_23]


title: CRBT184 [Oligo_les_22]


title: MG-Sal-WT-2F


title: MG-Sal-WT-1F


title: CRBT183 [Oligo_les_21]


title: MG-Sal-WT-3M


title: 2yr-KO-12M

value: 2 years

value: None/naïve


title: 2yr-KO-11M


title: CRBT181 [Oligo_les_19]


title: CRBT180 [Oligo_les_18]


title: MG-LPS-WT-1M

value: WT

value: LPS


title: 2yr-KO-10M

value: KO


title: CRBT192 [Oligo_les_30]


title: MG-Sal-KO-3F

value: F

value: Saline


title: 2yr-KO-9F


title: CRBT178 [Oligo_les_16]

value: Olig2-tdTomato TH39Gsat/Mmcd

value: brain (sub-ventricular zone and corpus callosum)


title: 2yr-KO-8F


title: CRBT177 [Oligo_les_15]

value: O


title: 2yr-KO-7F


title: 2yr-KO-6M


title: CRBT175 [Oligo_les_12]

value: 8-10 weeks old


title: CRBT176 [Oligo_les_14]


title: CRBT189 [Oligo_les_27]


title: 2yr-KO-4F

value: Microglia


title: CRBT174 [Oligo_les_11]


title: 2yr-KO-3M


title: CRBT182 [Oligo_les_20]


title: CRBT173 [Oligo_les_10]


title: 2yr-KO-2M


title: MG-Sal-WT-4M


title: CRBT172 [Oligo_les_9]


title: CRBT141 [ME_cont_73]

value: OligNB

value: OligNBL


title: 2yr-KO-1M

value: M


title: CRBT140 [ME_cont_72]

value: lesion


title: CRBT142 [ME_cont_74]


title: CRBT179 [Oligo_les_17]

value: OL


title: 2yr-Het-5M

value: Het

value: 2 years


title: CRBT138 [ME_cont_69]


title: 2yr-Het-8F

value: None/naïve


title: 2yr-Het-6F


title: 2yr-Het-3M


title: CRBT137 [ME_cont_68]


title: CRBT136 [ME_cont_67]


title: 2yr-Het-4M


title: 2yr-Het-1M


title: CRBT135 [ME_cont_66]


title: 2yr-Het-2F


title: 2yr-WT-10M

value: WT


title: CRBT134 [ME_cont_65]


title: 2yr-WT-9M


title: CRBT133 [ME_cont_64]


title: 2yr-WT-8F


title: CRBT131 [ME_cont_62]


title: 2yr-WT-7F


title: CRBT132 [ME_cont_63]


title: 2yr-WT-6F


title: CRBT139 [ME_cont_70]


title: 2yr-WT-5F


title: CRBT129 [ME_cont_60]


title: 2yr-WT-4M


title: 2yr-Het-7F


title: 2yr-WT-3F


title: 2yr-WT-2F


title: 1yr-KO-16M

value: KO

value: 1 year


title: 2yr-WT-1F

value: F


title: CRBT121 [ME_cont_52]


title: CRBT126 [ME_cont_57]


title: CRBT119 [ME_cont_50]


title: 1yr-KO-15M


title: 1yr-KO-14M


title: CRBT116 [ME_cont_46]


title: 1yr-KO-13M


title: CRBT127 [ME_cont_58]


title: CRBT115 [ME_cont_45]


title: CRBT130 [ME_cont_61]


title: 1yr-KO-3F


title: 1yr-KO-11F


title: CRBT113 [ME_cont_36]


title: CRBT114 [ME_cont_43]


title: 1yr-KO-8F


title: CRBT128 [ME_cont_59]


title: CRBT112 [ME_cont_38]


title: 1yr-KO-7M


title: 1yr-KO-6M


title: CRBT108 [ME_cont_24]


title: 1yr-KO-2F


title: CRBT109 [ME_cont_25]


title: CRBT123 [ME_cont_54]


title: CRBT107 [ME_cont_23]


title: CRBT124 [ME_cont_55]


title: 1yr-KO-1F


title: 1yr-Het-14M


title: 1yr-Het-12M


title: CRBT105 [ME_cont_21]


title: CRBT106 [ME_cont_22]


title: 1yr-Het-11M


title: CRBT103 [ME_cont_19]


title: CRBT102 [ME_cont_18]


title: CRBT104 [ME_cont_20]


title: 1yr-Het-8F


title: CRBT84 [NB_les_32]

value: NB

value: NBL


title: 1yr-Het-9F


title: CRBT110 [ME_cont_28]

value: brain (sub-ventricular zone and corpus callosum)


title: 1yr-KO-9F


title: 1yr-Het-7F


title: CRBT83 [NB_les_31]

value: 8-10 weeks old


title: 1yr-Het-5F

value: Microglia


title: 1yr-Het-4M


title: CRBT101 [ME_cont_17]

value: OligNB


title: 1yr-Het-1F


title: CRBT81 [NB_les_28]


title: CRBT79 [NB_les_26]


title: CRBT78 [NB_les_25]


title: 1yr-Het-6F


title: CRBT82 [NB_les_29]


title: CRBT80 [NB_les_27]


title: 1yr-WT-11M


title: CRBT77 [NB_les_24]


title: 1yr-Het-2M


title: CRBT75 [NB_les_22]


title: 1yr-WT-10M


title: 1yr-WT-6F


title: CRBT73 [NB_les_20]


title: 1yr-WT-9M


title: 1yr-WT-5F


title: CRBT76 [NB_les_23]


title: 1yr-WT-4F


title: 1yr-WT-8F


title: 1yr-WT-7F


title: CRBT72 [NB_les_19]


title: 1yr-WT-2F


title: CRBT74 [NB_les_21]


title: CRBT68 [NB_les_15]


title: CRBT71 [NB_les_18]


title: 1yr-WT-3F


title: CRBT69 [NB_les_16]


title: CRBT67 [NB_les_14]


title: 2mo-KO-13M

value: 2 months


title: 2mo-KO-12M

value: M


title: CRBT64 [NB_les_11]

value: lesion


title: CRBT63 [NB_les_10]


title: CRBT66 [NB_les_13]


title: 2mo-KO-11M


title: 2mo-KO-9M


title: 2mo-KO-10M


title: CRBT65 [NB_les_12]


title: 2mo-KO-7F


title: CRBT61 [NB_les_6]


title: 2mo-KO-8F


title: 2mo-KO-6F


title: CRBT60 [NB_les_5]


title: 2mo-KO-5F


title: PR_T60_R5020_MTVL_WT_ChIPseq

city: Autonomous CIty of Buenos Aires

first: Santiago

middle: Andres

last: Rodriguez Segui

address: Intendente Guiraldes s/n

country: Argentina

institute: IFIBYNE-UBA-CONICET

description:
ChIPseq on T47D MTVL WT stimulated cells for 60 minutes with R5020 (10 nM)
T47D MTVL WT cells (used as control in this work)

data_processing:
The raw sequence reads were aligned to human (UCSC hg19) genome using Bowtie (version 1.1.1). Only sequences uniquely aligned with ≤1 mismatch were retained.
Post-alignment processing of sequence reads included in silico extension and signal normalization based on the number of million mapped reads. Reads were extended to a final length equal to MACS (version 1.4.2) fragment size estimation, and only unique reads were retained.
For signal normalization, the number of reads mapping to each base in the genome was counted using the genomeCoverageBed command from BedTools.
Genome_build: hg19
Supplementary_files_format_and_content: Transcription factor enrichment sites were detected with MACS (version 1.4.2) using default parameters and a P value of 10-10. A control dataset derived by sequencing input DNA samples was used to define a background model.

source_name: T47D MTVL WT (Ctrl)

growth_protocol: T47D-WT and T47D/A1-2 cells were grown 48 h in DMEM without phenol red supplemented with 10% dextran-coated charcoal-treated FBS and synchronized in G0/G1 by 24 h of serum starvation.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: R5020 or DEX was added to the medium at 10 nM, and cells were harvested after 1 hour of hormone treatment.

value: Mammary epithelial cells

tag: chip antibody

value: anti-PR, H-190, sc-7208, Santa Cruz Biotechnology

tag: agent


title: PR_T0_MTVL_WT_ChIPseq

description:
ChIPseq on T47D MTVL WT unstimulated cells (Control)
T47D MTVL WT cells (used as control in this work)


title: 2mo-KO-4F


title: PR_T0_A1_2_ChIPseq

description:
ChIPseq on T47D A1/2 unstimulated cells (Control)
T47D A1/2 cells

source_name: T47D A1/2 cells

value: T47D A1/2 cells


title: PR_T60_R5020_A1_2_ChIPseq

description:
ChIPseq on T47D A1/2 stimulated cells for 60 minutes with R5020 (10 nM)
T47D A1/2 cells


title: CRBT58 [NB_les_2]


title: CRBT57 [NB_les_1]


title: GR_T60_Dex_A1_2_ChIPseq

description:
ChIPseq on T47D A1/2 stimulated cells for 60 minutes with Dex (10 nM)
T47D A1/2 cells

value: Mix:anti-GR, P-20, sc-1002, Santa Cruz Biotechnology and anti-GR, PA1-511A, Thermo Fisher Scientific

value: Dex (10 nM)


title: INPUT_A1_2

description:
INPUT DNA
T47D A1/2 cells


title: GR_T0_A1_2_ChIPseq


title: 2mo-KO-2M

value: KO

value: None/naïve


title: CRBT56 [NB_cont_48]

value: control


title: CRBT62 [NB_les_9]

value: NB


title: 2mo-Het-10M

value: Het


title: 2mo-Het-9M


title: 2mo-Het-7M


title: CRBT55 [NB_cont_47]

value: brain (sub-ventricular zone and corpus callosum)


title: CRBT53 [NB_cont_44]

value: 8-10 weeks old


title: 2mo-Het-6F

value: F

value: Microglia


title: CRBT54 [NB_cont_46]


title: CRBT59 [NB_les_4]

value: NBL


title: CRBT52 [NB_cont_43]


title: 2mo-Het-5F

value: 2 months


title: GR_T60_R5020_A1_2_ChIPseq


title: 2mo-Het-4F


title: CRBT49 [NB_cont_40]


title: 2mo-Het-3F


title: 2mo-Het-2M

value: M


title: CRBT48 [NB_cont_39]


title: 2mo-Het-1M


title: 7911747040_K: 15010-DAY6

city: Budapest

first: Gábor

middle: Nándor

last: Than

address: Magyar tudósok krt. 2

department: Institute of Enzymology

country: Hungary

institute: Research Centre for Natural Sciences

description: replicate 3, day 6

hyb_protocol: Labeled cRNAs were hybridized to HumanHT-12v4 Expression BeadChips.

scan_protocol: BeadChips were imaged using an Illumina BeadArray Reader, and raw data were obtained with Illumina BeadStudio Software V.3.4.0.

data_processing: Expression intensities were background-corrected using the default method in the lumiR function of the LUMI package. Data was variance stabilized via log2 transformation and normalized with the quantile method. From the 47,307 probes on the array, we included those 25,025 probes (14,197 unique genes) into the further steps of analysis which had at least two samples with a False Discovery Rate (FDR)-adjusted p-value of <0.1.

source_name: villous trophoblast culture, replicate 3, day 6

label_protocol: DNase-treated RNA samples (n=24; 500ng) were amplified and biotin-labeled with the Illumina TotalPrep RNA Amplification Kit.

growth_protocol: Placentas were taken from normal pregnant women delivering at term. Primary villous trophoblasts were isolated and plated on collagen-coated 12-well plates at 3x1,000,000 cells/well density in Iscove’s modified Dulbecco’s medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin.

extract_protocol: Total RNA was isolated from primary trophoblasts harvested on Days 0-7 of differentiation with RNeasy kit.

treatment_protocol: The effect of trophoblast differentiation on gene expression was tested by keeping primary trophoblasts in IMDM containing 5% non-pregnant human serum and 1% P/S for 7 days. The medium was replenished every 24h, and cells were harvested for total RNA in every 24h.

value: villous trophoblast

tag: differentiation day


title: 7911747040_G: 15010-DAY2

description: replicate 3, day 2

source_name: villous trophoblast culture, replicate 3, day 2


title: 7911747040_L: 15010-DAY7

description: replicate 3, day 7

source_name: villous trophoblast culture, replicate 3, day 7


title: 7911747040_H: 15010-DAY3

description: replicate 3, day 3

source_name: villous trophoblast culture, replicate 3, day 3


title: 7911747040_D: 14836-DAY7

description: replicate 2, day 7

source_name: villous trophoblast culture, replicate 2, day 7


title: 2mo-WT-11F

value: WT


title: 7911747040_C: 14836-DAY6

description: replicate 2, day 6

source_name: villous trophoblast culture, replicate 2, day 6


title: CRBT46 [NB_cont_37]


title: 7911747040_I: 15010-DAY4

description: replicate 3, day 4

source_name: villous trophoblast culture, replicate 3, day 4


title: 7911747040_F: 15010-DAY1

description: replicate 3, day 1

source_name: villous trophoblast culture, replicate 3, day 1


title: 7911747040_J: 15010-DAY5

description: replicate 3, day 5

source_name: villous trophoblast culture, replicate 3, day 5


title: 7911747040_A: 14836-DAY4

description: replicate 2, day 4

source_name: villous trophoblast culture, replicate 2, day 4


title: 7911747040_B: 14836-DAY5

description: replicate 2, day 5

source_name: villous trophoblast culture, replicate 2, day 5


title: 2mo-WT-10F